In the process of inter-organizational cooperation in knowledge aliiance??Cthere exists two power structures, which are core enterprise-led structure and agent-led structure. Our research indicates that in the two structures??Cthe agent's required unit pay of innovative products is positive correlation to its marginal innovative cost, and is negative correlation to its technical capacity growth earnings. The core enterprise's optimal marginal profit is negative correlation to the agent's marginal innovative cost, and is positive correlation to the agent's capacity growth earnings. Under the situation of the agent-led structure, if the difference between the agent's unit innovative cost and capacity growth earnings is little, the agent's required pay is higher than pay of the core enterprise-led structure, and the core enterprise's marginal profit is lower than profit of the core enterprise-led structure, and vice versa.