In the early 20 century, interdisciplinary research (IDR) arised in the production of scientific knowledge. And after World War Two, the social problems became so complex as to require insights from multiple disciplines, and IDR increasingly inspired by drives from outside universities. With stepping out of the Tower for social responsibilities, universities developed more and more IDR, and centers and institutes as the organizational forms of IDR increased rapidly. But in reality, IDR in universities is confronted and so discouraged by many obstacles and conflicts. What are they and the reasons behind them? How to harmonize? That is the starting-point of the whole study.Discipline is a body of knowledge, and IDR requires integrating two or more disciplines or bodies of spe-cialized knowledge. Multidisciplinarity, pluridisciplinarity, interdisciplinarity and transdisciplinarity are classified by the degree of integration. From the perspective of epistemology, the difference between modernism and postmodernism exists in IDR.Each disciplinary culture comprises its own values, methodology, language, style and identity, and differences and conflicts emerge between disciplinary cultures when disciplines integrated. There are different mechanisms and types of IDR, and the relationship among related disciplines appears so complicated according the nature of the disciplines, which shows the inner complextity of IDR in the aspect of disciplinary culture. To facilitate IDR, open disciplinary boundaries, common IDR paradigms, equality and confidence are needed, and a cognitive framework based on common ground is required in the process of IDR for the dialogue and communication among disciplines.Disciplinary organizations are basic units in universities, which embody the boundaries of knowledge and have characteristics of bureaucracy. Obstacles and conflicts exist in IDR in the aspects of different disciplinary organizational goals, structures, powers and member roles. In universities, matrix-based IDR organizations are structured within the bureaucracy, and get a balance between centralization and decentralization. Director liability, participated management and shared leadership are the main managing ways within the organizations of IDR. To overcome those obstacles and conflicts, IDR organizations must form the common goals, open organizational boundaries, have IDR as an emphasis in research policy and put it under the level of the whole university. Furthermore, the governing way of academic committee can facilitate to clear up the conflicts from academic powers, and that of executive committee can help to clear up those from administrative powers. And finally, the conflicts of member roles and identities require a process of self-tuning and external coordination. These countermeasures are well validated in the case analysis of California University, the University of Tokyo and Media Lab in MIT.The conflicts of interest between different disciplines are fundamentally discouraging to IDR. Fundings inside and outside universities, faculties and facilities are allocated to discipline-based colleges and departments, and these obstacles together with the complexity and risk of IDR lead to insufficient resources for IDR organizations. Independent budget, seed money and program aiding need to be established and even institutionalized to assure the abundance of funding for IDR. Still, universities should establish a matrix funding system, faculty joint appointment and indirect cost recovery to create a good environment for IDR. Evaluzation has a steering role in the allocation of resources, so it is important in IDR. But based on single-discipline, the traditional evaluation produce obstacles to IDR, and its main form is peer review. So the key issue is to change the system of peer review, focusing on the standards, principles, methods and procedures of evaluation and related administration system.Two routes are in the paper for the whole research, one is from a perspective of disciplinary culture, the other disciplinary organization, which is applied to analyze the obstacles and conflicts in IDR and seek the ways to clear them up. The obstacles and conflicts from disciplinary cultures are difficult to remove, but a deep understanding of them is necessary in IDR. In practice, universities take emphasis for reengineering the organizational structures, but lack instititutional changes. In the coming future, universities may shift to institutionalization to facilitate IDR.