In order to improve the productivity of applied research, governments have generated large-scale research funds for establishing new centers to promote collaboration between internal/external organizations and researchers with different specialties. However, it is challenging for universities and public institutes to develop the strategy, operational process and organizational structure for maximizing the effect of collaboration. Due to the lack of standardized methods for measuring the performance of research projects with integrative approaches, it is still difficult for the governments to evaluate the outcome of each project and effectiveness of the research funding. In this research, we have conducted the comparative research between two of the largest research programs in Japan with a strong focus on integration of interdisciplinary fields, Center for Nanobio Integration (CNBI) of The University of Tokyo and Institute for Integrated Cell-Material Sciences (iCeMS) of Kyoto University by database analysis and questionnaire survey of researchers, aiming at identifying key success factors of management of interdisciplinary projects and requirements of individual researchers who could promote collaboration and integration. Through these empirical approaches, we have obtained several implications for the effective institutional management and developed a managerial framework for measuring and evaluating the outcome of the interdisciplinary research projects.