The science and technology cooperative innovation in Beijing-Tianjin-Hebei is an important part of the cooperative development strategy in China. Cross-regional and complexity are the typical characteristics. The cooperative innovation is affected by many factors，such as government’s policies，innovation resources，and innovation actors. So，it needs to establish the coordination mechanism between the governments，the mechanism of benefit sharing and compensation the participation mechanism of the main actions from macro，intermediate and micro level to form three-dimensional governance structure.