The purpose of the current study is to investigate the current situation of pathogenic microorganism laboratory in Shanghai disease control institutions, analyze the biosafety situation of the laboratory, and put forward countermeasures and suggestions for further strengthening and standardizing the biosafety management of laboratories in Shanghai. Investigate the biosafety status of pathogenic microorganism laboratories in 16 district level disease control institutions in the field testing. It was found that the allocation rate of biosafety cabinet, autoclave, eye washer and UV lamp reached 100%. The biosafety cabinet and UV lamp are well maintained and the qualified rate of eye washer and autoclave is 87.50%. Among them, the indicators of the management system have been completed well, and the indicators of personnel management and experimental process management need to be improved. The compliance rate of residual chlorine monitoring values in wastewater treatment is lower than 80%. The results show that the establishment of biosafety system and the implementation of laboratory responsibilities are well completed, and waste disposal, facilities and equipment management, and emergency plan system need to be further improved and improved.