In today's rapid economic development, people's demand for logistics is getting higher and higher. Through constructing the evolutionary game model of government and manufacturing enterprise, the equilibrium mechanism of co-evolution was studied and verified by Matlab. The result shows that the main reason of logistics service innovation in manufacturing enterprises lies in their income and expenses. On this basis, the policy encouragement can effectively promote the innovation. In view of the current situation of our country's manufacturing enterprises, some countermeasures are put forward to strengthen the government incentive and promote the development of logistics services.