Nitrogen is the important growth source of biological living on earth. Human being study and utilizes nitrogen from biosphere development and satisfaction of food needs all the while. With the increase of fertilization, nutrient matter loss has become the main reason of eutrophication of the inland lake. Excess nitrogen in the field from using fertilizer, being partially lost through ammonia volatilization and denitrification, can become important greenhouse gas and affect the atmosphere quality and ecological balance. Agriculture non-point source pollution has received much attention today.A field experiment was conducted in a paddy-wheat planting soil in the support of Shanghai. Base on the soil- crop- water systems as the overall object of study, discusses the nitrogen changes , cycles, balances process and the characteristic between every sub-system under field condition, and estimates the total N loss in the paddy-wheat planting and effect to the water environment. The main conclusions can be summed up as follows:(1) There are the different characteristic at the motion and direction of soil water in process of paddy- wheat rotation. In paddy season, the main saturation motion is under water-flooding condition, while the dominating motion is unsaturated motion by affection of rainfall in wheat season. The study result indicates that the runoff and leaching both in paddy and wheat season are relate with rainfall and show the characteristic happening randomly, while they also appear law characteristic under the given soil and environment condition. There is obvious index correlation between rainfall runoff and rain fall in paddy and wheat season, meanwhile, the linear correlation between rainfall and leaching in soil is also very clear in wheat season.(2) Oxidation-reduction changing alternately in process of paddy- wheat rotation is the main element for controlling and affecting to the result and direction of nitrogen conversion in soil. The form and concentrations change of nitrogen in the soil profile also influence changing of soil water. Because of the frequent irrigation in paddy season, the reduction is strong and the NH_4~+-N of soil cannot convert to the NO_3~--N in soil, the seasonal change of NO_3~-N in the soil profile is small and the range is from 0.95 mg/kg to 6.42 mg/kg. Fertilization or not is not have significant difference. However it changes to oxidation condition and nitrification is enhanced in wheat season. The content of NO_3~--N with fertilization is obvious change both in season and soil profile. The range of the concentration is from 1.22 to 15.2 mg/kg. Because of soil matter has strong adsorption ability to NH_4~+-N, during the whole paddy-wheat rotation, the N fertilizer is main influence the change and transform of NH_4~+-N in surface soil and little of them move down. Under using abio-fertilizer only, NH_4~+-N and NO_3~--N in soil do not cumulate obvious at the front and end of cultivate and the total N changes slightly. There is not evident influence to the level of nitrogen fertility in soil. (3) Because of soil matter has strong adsorption ability to NH_4~+-N, during the whole paddy-wheat rotation, the concentrations of water in soil profile is low all, most of them lower than 1 mg/L.The concentration of NO_3~--N is lower in the water of soil profile in paddy season, leaching is not obvious. The change concentrations of NO_3~--N in soil water with fertilization is markedly, from 0.09 to30.58 mg/L. The 76% of NO_3~--N concentration in soil water are exceed 5 mg/L above 60 cm of soil and 51% of that exceed 10 mg/L. with the characteristic of leaching, concentrations of NO_3~--N at shallow groundwater(120 cm) increase in different degree.(4) The N loss from farm relate to the factors about the amount and species of fertilizer, the texture of the soil, the rainfall, the hydrology conditions, cultivation, management and vegetation. From these, fertilizer and rainfall are the basic factors of effect, redox condition of the soil is different tent to form and concentration of nitrogen in the surface runoff and leaching are different in paddy and wheat season. NH_4~+-N concentration is higher during the first week after fertilizer and affect the quality of water environment in paddy season. The N loss both of runoff and leaching are affected by the fertilization and have high concentration and great loss in the wheat season's rainfall. It severity affected the quality of groundwater and surface water. It was the main N pollution source in process of paddy- wheat rotation.(5) The N loss of surface runoff is a key process from farm. A math model was developed according on the rule of NH_4~+-N loss of surface runoff from this experiment. The model simulated the process and transform of the surface runoff. The results are very approach the real experiment date: the R is 0.89 and 0.99, respectively. This model's parameter and date is considered easily to get from production process. Since it can also calculate conveniently, it's a good math model to predict and control the NH_4~+-N loss of surface runoff from farm.(6) On two years' monitor and analysis of the paddy- wheat rotation, over fertilization and irrational cultivation and management is the main reason of N loss from farm. In order to reduce the pollution environment, the technique of fertilizer, increase the efficiency of fertilizer using, introduce irrigate technique, and other techniques should be improved, related law and regulations be established, education and propaganda be done and efficient encourage measure be mapped out to protect the environment.(7) Adopting N income and expenses methods to study the N-balance character in the farm system. The results show that the N's apparent recovery is between 59% and 78%, paddy is a bit higher than wheat. The N loss with farm water outflow is comparatively low, about 2% and 7% in paddy and wheat season, respectively. The gas loss is higher in 25% and 29%. So the gas loss is the key way of N loss in paddy-wheat rotation from farm and the important pollution source of atmosphere pollution.