Abstract:The profit sharing mode is the main incentive mechanism used during the process of industry-university collaboration innovation under principal-agent relationships. The agent can be encouraged but rather limited, depending on the external force (e.g. the government subsidy) may be the only way to get additional encouragement. Based on the principal-agent theory, we use continuous Cobb-Douglas production function, we find the subsidy mode of subsidy to the agent according to the cost, which can stimulate the agent more effectively and give the quantity of subsidy quantitatively. Under this method, the effort which the agent wants to make is just the effort the maximum collaboration profits wanted. When the subsidy increases, the trend of the collaboration profits appears to be three stages: accelerated growth stage, decelerated growth stage and negative growth stage. Fewer subsidies lead to higher acceleration of profits, while more subsidies lead to lower acceleration of profits and higher probability of moral hazard. Synergistic effect is found when subsidy exists, although the subsidy is given to the agent. The principle is also encouraged, which makes the collaboration profits higher.