The current test system for a certain type of missile has insufficient coverage for the calibrating/ leveling/collimating combination test, thus a new intelligent fault detection system was designed. In the system, synchronization detection of software and hardware based on the feature point coverage is adopted, and modular design based on PC104 bus is used for the hardware modules. The system is compact and portable, and has the characteristics of high fault detection speed, high intelligence, and comprehensive fault detection coverage.