Abstract: Based on the feasibility basis of the collaborative innovation of ecological agriculture between Fujian and Taiwan, the dynamic mechanism model which was composed of two main systems, namely the endogenous drive and the outward transmission was built according to the different roles played by the internal and external factors. Then, from the perspectives of integration and interaction, the path choices were proposed including communicating fully to share the innovative knowledge, coordinating with each other to optimize the resource allocation, collaborating with each other to seek the optimal synchronous behavior, and collaborating comprehensively to achieve the high-level system matching.