Since the launch of the 4th Science and Technology Basic Plan in Japan, contributing to the development of innovation ecosystem has become a core objective of industry-university-government cooperation. In order to comprehensively and systematically grasp the cooperation mechanism of Japanese "industry-university-government" in promoting the construction of innovation ecosystems in depth, this paper analyses the three aspects of driving factors, planning and design, and on-the-ground practice,and takes the construction and implementation of the "Tsukuba Innovation Ecosystem", which has been rated as an excellent project in the Regional Innovation Ecosystem Construction Plan, as a case study, and analyses its mode of operation in concrete terms.The analysis results show that, in terms of innovation drive, science and technology innovation as the interest linkage of the main body of industry-university-government cooperation has driven the government, universities and industries to continuously and deeply participate in industry- university- government cooperation activities;and in terms of institutional initiatives, the Japanese government has advanced and optimized its policy on industry-university-government cooperation by constructing the "University-Industry-Government" knowledge circulation system,increasing the scale and effectiveness of industry-university-government cooperation, strengthening and widening the bridges between industry-university-government cooperation, and accelerating the deeper integration of cross-border actors.The case studies show that planning and designing based on regional advantages, strengthening intermediary forces to promote cross-border interactions, and facilitating synergistic operations to realize the iterative cycle from knowledge production to innovation and manufacturing are the practical features of Japan's industry-academia-government cooperation.Drawing on Japan's experience, in the future, China's industry-university-research collaborative innovation should be promoted by establishing a perfect mechanism for the integration and development of industry-university-research at the top level, promoting the construction of a multi-dimensional collaborative innovation cooperation in terms of the main driving force, giving full play to the role of the university's knowledge production in terms of the core of the driving force, and focusing on the introduction of an intermediary co-ordination force in terms of the operational guarantee.