Objective To explore and analyze the factors affecting the quality control of microbiological laboratories in the Centers for Disease Control and Prevention and the countermeasures.Methods: A total of 120 microbiological samples collected from the Centers for Disease Control and Prevention (CDC) from May 2020 to May 2022 were included in the routine management, while the control group included 60 samples not under quality control from May 2020 to May 2021.A total of 60 samples undergoing quality control from June 2021 to May 2022 were included in the study group.The probability of quality problems in the two groups was compared through relevant statistics, and then the relevant factors affecting quality control were analyzed.Results: The probability of sample quality problems in the research group with quality control management was 3.33% which was significantly lower than 16.67% of the reference group (P < 0.05).The analysis showed that personnel were the main factors affecting the quality problems of study group, while the factors affecting the quality problems of reference group were personnel, environment, instrument, operation and sample, among which personnel was the most important factor while sample was the least.Conclusion: The probability of quality problems can be significantly reduced by quality control management of microbial laboratories in CDC.Therefore, CDC should pay attention to quality control management, and improve and optimize the problems after a comprehensive analysis of the relevant factors affecting quality control.In view of the high impact of personnel, the comprehensive literacy of inspectors should be continuously improved, and the standardized management of various instruments and equipment should be strengthened in order to minimize the incidence of quality problems and further improve the accuracy of testing.