In this paper, we have proposed a methodology which can make effective test for system integration of complex guided missile system. System integration test play a significant role in the development of weapon system, providing the means to detect and isolate faults on first linkage between sub-systems. Integration tests for domestic weapon system has executed not a technology-intensive method based on tool but labor-intensive method based on experience. Higher cost, longer period, and more resource are required to execute system integration test for complex guided missile system comparing with past weapon systems, because recently weapon systems have more complex and more networked functions. Because the proposed design method for system integration test decreases number of test case, it lead to a decrease of cost, period, and resource for integration test of weapon system. The proposed configuration for system integration test will ensure reliability through detection and isolation of fault on linkage between sub-systems.