Public-Private Partnership (PPP) is an important mode to upgrade the level of public service through the cooperation between public sectors and private sectors. Based on the background of PPPs in medical and health fields in China, cooperative involvement and cooperative embedment that the pharmaceutical enterprises have cooperation with the non-profit organizations and its influence towards the cooperation efficiency were studied by incomplete contract theory. Firstly this paper establishes the mathematical model of cooperative involvement and cooperative embedment and its influencing s the cooperation efficiency is established. Basic research hypotheses are proposed. The results show that the cooperative involvement and cooperative embedment do have influence on the self-interest investment and the public-interest investment of the enterprises in PPP, on the one hand, higher level of the cooperative involvement and cooperative embedment will ensure the enterprises to choose the less self-interest investment and more public-interest investment to satisfy the condition of incentive compatibility，on the other hand it can enhance the PPP's efficiency.