[Background] Due to the serious public safety problem caused by the propagation of pathogenic microorganisms, such as Ebola virus, the governments of all countries pay much attention to laboratory biosafety. [Objective] To assess the safety status of pathogenic microorganisms in Chinese universities will benefit for the specific-targeted laboratory management measures. [Methods] Based on literature review and interview with some experts of biosafety management, we designed the questionnaire and the investigation was carried out with the participation of 341 technicians and students from 50 Chinese universities. [Results] Some important steps for management of pathogenic microorganisms were obvious insufficient, especially in biosafety education, establishment of safety management system, construction of standardized laboratory, biological waste disposal, and laboratory safety facilities maintenance. [Conclusion] The universities should put safety construction responsibility into effect so as to eliminate the above latent dangers of safety hazards.