Abstract: From the angle of system engineering methodology, logistics safety evaluation system was used to evaluate logistics system, which involves the general steps, the specific stages, the relative knowledge and the environmental impact assessment. Based on the 3-dimensional structure of Hall, a 4-dimensional structure of logistics safety evaluation system was built. On this basis, a holistic structure model for logistics safety evaluation system was constructed, and specific implementation steps for logistics safety evaluation system were expounded in detail. Finally, the evaluation system was applied to the safety assessment of logistics information system, and the assessment result indicates that the evaluation method is feasible, meanwhile, related safety countermeasures were proposed. The system provides a new idea for the logistics safety evaluation, and a foundation for the construction of the more practical logistics system safety evaluation system and evaluation methods.