In response to the problem of increasing air traffic flow, complex air conditions and sudden increase in flight safety under free flight, the minimum safe distance model for different aircraft types is proposed based on the risk of aircraft collision. Firstly, we focus on the influence of CNS performance, human factors and high altitude wind on aircraft flight, and derive and construct a comprehensive collision risk model to find the minimum safe distance that meets the safety requirements by using segmentation finding interval method. Secondly, different distances and flight scenarios are set, and the Monte Carlo method and MATLAB are used to simulate the cases to verify the safety and validity of the model. Subsequently, the relationship between the minimum safe distance and the variation of parameters of different influencing factors is obtained through experimental simulation. Finally, it is shown by comparing different computational models that the model can effectively reduce the minimum safety distance, which provides new ideas and methods to promote the further development of free flight.