Abstract:The general system module theory is a new modern system theory which inherits and develops the general system structure theory. It puts forward the concept of "independent module", which makes the system innovation and collaborative innovation mechanism have the independent basis of modules. Based on the theory of general system modules, the paper explains the operating mechanism of the collaborative innovation system and summarizes module independence, cohesion and coupling, polymorphism, partnership four main operating tracks. On this basis, from the macro perspective to the micro subject, the paper proposes four suggestions for the collaborative innovation subjects, including breaking the boundary, clear rights and responsibilities, deep cooperation and innovation mechanism.