The purpose of the current study is to study the effect of in-hospital three-color zoning management mode in SARS-CoV-2 nucleic acid sample collection during the epidemic. Patients and staff involved in nucleic acid sample collection in our hospital during April 1 st to 15th April, 2022 were selected as the control group, and the original nucleic acid sample collection mode was adopted. Patients and staff involved in nucleic acid sample collection During April16th to 30th April, 2022 in our hospital were regarded as observation group which adopted the three-color zoning management mode. Compared with the control group, the whole time of nucleic acid sampling-transport-testing in the red zone (all P<0.05), the detection time (P＝0.024) and detection time (P<0.001) and the tracing time of patients with nucleic acid abnormalities (P<0.001) were significantly shortened in the observation group. Conditions of unqualified samples were significantly reduced (P＝0.001), including sample leakage (P＝0.018), lack of internal parameters (P＝0.012), and information errors (P＝0.014). Patient (P<0.001) and staff (P<0.001) satisfaction increased significantly. The three-color zoning management model can effectively shorten the time consumption of sampling-transporting-testing of nucleic acid sample collection and of the tracing of patients with nucleic acid abnormalities. This mode improved work efficiency, and the quality of nucleic acid samples, and satisfaction of patients and staff.