The integration of military and civil aviation is an important driving force for implementing innovation-driven development and promoting national and regional economic development. However, the integration of military and civil aviation with only the participation of the military and civil aviation has various drawbacks. In order to promote the integration of military and civil aviation, this article discusses the evolutionary game of military and civil aviation integration under policy intervention, and establishes a tripartite evolutionary game model with the government, the military, and civil aviation as the main stakeholders. Matlab software is used to analyze the strategy selection of each entity and its game equilibrium problem, solve the evolutionary equilibrium strategy and conduct numerical simulation analysis, and then analyze the evolution trend of each entity under the influence of the choice strategy intention of the other two entities. The results show that the government, the military, and civil aviation are affected differently by each other’s willingness to participate; different incentive mechanisms of the government have different impacts on the military and civil aviation; and civil aviation is more sensitive to penalty intensity and income distribution.