Before final assembly and while debugging a missile, in order to ensure the flight control system can work stably and reliably, it is necessary to develop an auto test system. Test software is an important part of the test system. After describing the composition and working principle of the flight control system, summarizing the test requirements, the test software is designed. The design ideas, test algorithm, realization and key technologies, software anti-jamming techniques are introduced in detail. The test software guarantees the test system test the flight control system generally and reliably.