Objective To establish HACCP system in canteens in High School District and analyze its effectiveness, in order to set an example for carrying out HACCP in other student canteens of the Corps in Xinjiang. Methods Hygienic investigation was carried out by questionnaire survey, laboratory testing, data comparison and other methods to analyze the effectiveness of applying HACCP system in student canteens. Result Health knowledge of practitioners has been improved significantly, the quality of air in operating room was not significantly different (P>0.05), the detection rate of aerobic bacterial count in food processing sectors was reduced significantly (P <0.05), the qualified rate of coliform bacteria was significantly improved (P<0.01), the qualified rate of tableware disinfection was 100% before and after implantation of HACCP. Conclusion The effectiveness of establishing HACCP system in the High School District is evident, operations on food processing are more standardized in ensuring food safety.