Objective  To explore the disinfection method of disinfectant in clean area and ensure effective disinfection of clean area. Methods   Bromogeramine and peracetic acid were used to disinfect the clean area, the microbial limit was detected, and disinfectant residue was tested. The influence of disinfected area, materials of contact surface, and disinfection time on disinfection effect was examined. Results  With either disinfectant, replacing the cleanroom wipers fulfilled with  disinfectant every 4 m² and disinfectant contact with the clean interface for 5 min obtained the best microbial elimination effect. After the second wipe with detergent, the residual amount of disinfectant did not affect human health and product quality. Conclusion  A suitable method for disinfection in clean areas was established.