The research analyzed the material treatment, career management, welfare, and other incentives for researchers in Japanese universities, research institutions, and enterprises. It concluded that the complementary relationship of research collaboration among Japanese universities, research institutions, and enterprises, leveraging their respective strengths, has played an important role in promoting the development of scientific and technological innovation in Japan. Japan's scientific research is well-funded, with diverse sources of funding. Additionally, Japan's research funds are allocated clearly and competitively, ensuring the high-quality development of its scientific research. While optimizing the efficiency of research funding allocation and other measures, Japan focuses on increasing opportunities for young scholars to obtain research grants, providing more possibilities for the future development of science in Japan. The stable and diverse income sources, combined with scientific management methods, have improved the welfare of researchers and promoted the formation of incentive mechanisms. This study of the current situation and its characteristics has important reference significance for China in optimizing the incentive system of its fundamental research team.