According to the characteristics of various trajectory forms and complex control law of air-launched anti-ship missile, the trajectory design and simulation realization of the trajectory in different flight stages are studied from the perspective of low-altitude cruise trajectory of anti-ship missile. The common trajectory types, characteristics and technical performance of air-launched anti-ship missile are analyzed. The simulation model of longitudinal motion trajectory of anti-ship missile is established by using Matlab/Simulink. According to the design of low altitude cruise trajectory in the flight phase, the PID control is used to realize the attitude and altitude stability control of the missile; in the terminal guidance phase, the over-gravity compensation proportional guidance method is used to realize the terminal jump and dive attack of the missile. The simulation results show that the design method can realize the preset trajectory well, and provide a reference for the trajectory design and analysis of air-launched anti-ship missile.