Abstract:The further reform of scientific research management system and implementation of innovation-driven developing strategy has brought great challenges to the current management of scientific research system. A new matrix management of scientific research system based on collaboration team has been proposed according to previously practical experience of Institute of Nuclear Energy Safety Technology, Chinese Academy of Sciences. A new matrix management, which was organized in "research dimension", "administration dimension" and "project dimension", could maximize the outputs based on the synergy of different resources. The formation and framework of the management were introduced in this paper, and also the achievements due to its applications.