Collaborative innovation across administrative regions is an important way to achieve major national strategies and enhance the core competitiveness of regional and industrial brands. It is of great significance to the transformation and upgrading of China"s economic structure and the realization of high-quality development goals. The basis for the effective operation of collaborative innovation across administrative regions is the construction of a collaborative innovation platform. This paper analyzes the evolutionary characteristics of the linkage mode of the collaborative innovation subject, describes the functions of the cross-administrative regional collaborative innovation platform based on the connotation of the cross-administrative regional collaborative innovation platform, designs the subsystems of the cross-administrative collaborative innovation platform service system and its platform organization structure, and then, designs the platform operation mechanism. It is expected to provide a reference for the cross-administrative district collaborative innovation layout and the optimization and upgrading of regional innovation systems.