The article mainly introduced the application of GC/MS/CPU technique in navy military medicine. Firstly, qualitative study of components existing in the air of navy special environment and qualitative analysis of hazardous substances produced in special circumstance and on special conditions; Due to the study, the number and classification of the components in the air could be made clear, the source of air pollution and pathway could be found, varying rule of concentration could be made obvious, and the aim of overall assessment and control of the air quality could be realized. Secondly, analytical study of released substances from nonmetallic material used by ships; the study was fundamental work for assessment of ship-used material toxicity of ship-used materials and presented data for modeling, screening and first choice of the material. Thirdly, qualitative analysis of some special substances from crew`s metabolic products; the study was the key to studying effects of hazardous materials on crew`s body. Pathway of the materials entering the body, mechanism and metabolic process might be made clear by the study, which could presented bases for prevention and treatment of crew`s special disease. Fourthly, analysis of ingredients and structure of drugs and health-care food; the study was to present necessary technique consults for research, development and production of new products.