Reactor protection system (RPS) plays critical role in digital control system (DCS), and ensures the safety for nuclear power plant (NPP). System test is a necessary step during system development, verification and validation (V&V), which ensure the safety and reliability for RPS. The debugging of test environment and equipment is an important step that ensures the effective and efficiency of test. The system, such as RPS that contains complicated logic and large number of interfaces, cost a lot of time and human resource for debugging. A structured debugging method has been proposed in this paper, this method establishes debugging architecture with a hierarchical model in according to signal transmission path, and it designs the debugging process from down to top. The result from engineering practice show that this method has improved the effective and efficiency of debugging provides the support and reference for system test environment establishment.