Associated with a very high degree of association for manufacturing and logistics industry, the interactive development for them is very essential to enhance the competitiveness of the manufacturing industry and the service efficiency and ability of the logistics industry. After considering the compensate factors for the breakdown of cooperative relationship, this paper uses the classical analytical methods of the principal-agent theory, builds an implant compensation variable incentive model, analyzes the optimal decision problem and related factors of manufacturing and logistics companies. Results show that considering compensation factors, it could induce logistics enterprises to improve the level of effort and reduce the ruptured probability of cooperation, and it is very beneficial for them to establish better interactive and achieve fusion development.