A software system for a complex object scattering analysis, named SYSCOS, has been developed for a systematic radar cross section (RCS) analysis and reduction design. The system is based on the high frequency analysis methods of physical optics, geometrical optics, and physical theory of diffraction, which are suitable for RCS analysis of electromagnetically large and complex targets as like naval ships. In addition, a direct scattering center analysis function has been included, which gives relatively simple and intuitive way to discriminate problem areas in design stage when comparing with conventional image-based approaches. In this paper, the theoretical background and the organization of the SYSCOS system are presented. To verify its accuracy and to demonstrate its applicability, numerical analyses for a square plate, a sphere and a cylinder, a weapon system and a virtual naval ship have been carried out, of which results have been compared with analytic solutions and those obtained by the other existing software.