The navigation information of warship platform makes influence on navigation equipment accuracy, analyze the factor which makes influence on tracking accuracy of flight system. Analyze the satellite navigation equipment export time, influence of positioning error and attitude accuracy on radar and infrared warning equipment tracking accuracy. Discuss the influence of navigation equipment on tracking ability of fight system. Use heading angle data of navigation equipment to carry out measurement and verification. The analysis results show that the research can provide the reference for low tracking accuracy of warning detection equipment.