In order to discuss the cooperation between logistics nodes at different levels, a two-stage evolutionary game model was constructed to seek the equilibrium conditions of cooperation between nodes cities supported by superior governments from the macro level, and the equilibrium conditions of cooperation between nodes cities at the same and different levels from the micro level. Taking Liaoning province as an example, the equilibrium conditions of cooperation between nodes cities were analyzed. The results show that it is most ideal state for the superior government to adopt the encouragement policy for the node cities. The cooperative strategy chosen by the node city largely depends on the parameters size originated from the superior government. By changing the initial state of the game, adjusting government subsidies and common benefits, the cooperation of the logistics node city government can be realized. On this basis, relevant suggestions and measures are put forward to provide decision-making reference for cooperation between logistics node cities.