In order to overcome the shortcomings of the existing modeling and analysis methods in system modeling and performance analysis in flight mission, a method is proposed to establish a flight mission process model and study the operation process of a general aviation aircraft from the mission point of view. Combined with the ergonomic analysis and logical relationship of flight mission, a method of flight mission modeling and performance analysis for general aviation aircraft is proposed based on colored Petri net (CPN) theory. The flight mission model is established by CPN Tools, and the isomorphic Markov chain is constructed based on the model to solve the main performance indicators of the model, and the effectiveness of the method is verified by an example. The results show that the method can describe the flight mission control process clearly and intuitively, and can provide data support for flight mission design and flight safety.