This study aims to investigate the potential safety hazards and provide reference for improving the medical waste disposal procedure in SARS-CoV-2 testing laboratory. Our SARS-CoV-2 testing group detected the RNA residue on the surface of medical waste with Droplet Digital PCR, and held a meeting to discuss the risks in the laboratory medical waste disposal process. After effective autoclaving, SARS-CoV-2 contaminated on the surface of medical waste bags was killed, but the average concentration of viral RNA residues was still 0.85 copies/cm2. It would not pose a health risk, but might contaminate the laboratory and affect the test results. When the sterilized medical waste bags were transferred directly by the operators without hand disinfection, re-contamination would happen, which might cause the virus to leak out of the laboratory. Furthermore, we found that sterilization effect monitoring and cooperation among operators were also very important. In summary, we investigated and analyzed the potential safety hazards during the medical waste disposal process in SARS-CoV-2 testing laboratory, and provided reasonable suggestions to ensure the safety of medical waste disposal.