Abstract:As inter-organizational projects face challenges in cooperation and coordination, the related multi-agent periodic cooperation issues need to be resolved urgently. Based on the perspective of bounded rationality, the factors affecting the collaborative governance mechanism are analyzed from the life cycle of project generation, development, operation, disintegration, etc., and a multi-agent collaborative governance framework of inter-organizational R D project is established. Increased external temptation and decreased corporate reputation will reduce the stability of the cross-organizational project cooperation alliance system. Through qualitative and evolutionary analysis, attention should be paid to controlling costs during the development phase, rational distribution of benefits during the operation phase, and aftercare issues during the disintegration phase, providing background factors and theoretical support for the management operation mechanism and relationship coordination mechanism.