To provide constructive suggestions for the further improvement of the national standard (GB 4789) by evaluating the current food microbiological examination methods system. Methods The study was conducted by the means of questionnaire surveys in 19 provinces and municipalities which were located in the central and western regions of China. The subjects of the study were mainly the government inspection agencies, the enterprise inspection departments and the third party laboratories. The data was collected through an online system and analyzed by SPSS 22.0 and Microsoft Excel 2013. Results A total of 1 056 valid questionnaires were collected in the survey. The government and the enterprises were the subjects of the investigation. The overall score from different agencies were above 4 within a 5 point scale, and the enterprise inspection department’ score was higher than that of the government inspection agency (P<0.05). It was believed that 93.8% (991/1 056) of the respondents thought that the current standard system could fully or basically meet their needs. In terms of the improvement of standard system, 50.7% (535/1 056) of the respondents thought that it was urgent to revise the sample pretreatment method; in the aspect of increasing specific examine methods, different institutions had different ideas (P<0.05); as for rapid test method, 92.4% (976/1 056) of the respondents thought that it was necessary to include rapid test method in the microbiological examination methods system. Conclusion Food microbiological examination standards (GB 4789) system was frequently used, and the overall evaluation was good. It was suggested that the authorities should make clear the position of the rapid test method in the national food safety standard system and provide guidance for its development.