Objective To explore the effect of methyltransferase like protein 16 (METTL16) target⁃regulating small molecule compound phloretin and epigallocatechin gallate (EGCG) on HIV⁃1 replication. Methods (1) Two categories of small molecule compounds related to METTL16 target were screened by employing the high throughput computer bioinformation screening technique, namely, phloretin and EGCG. (2) Non⁃small cell lung cancerous cells A549 were used to perform screening experiment on compounds. A549 cells were assigned to blank group (only containing medium), control group (containing medium and A549 cells), or experiment group (containing medium, A549 cells, and 20 μmol/L phloretin/EGCG). After 24⁃hour intervention, the CCK⁃8 method was used to measure relative activity of A549 cells in various groups. (3) MT⁃2 and TZM⁃bl cells were assigned to blank group (containing medium), control group (containing medium, cells), or experiment group (containing medium, cells, and 5 concentrations of phloretin/EGCG). After 24⁃hour intervention, the number of living cells was detected through the ATP fluorescent quantitative analysis method. (4) MT⁃2 and TZM⁃bl cells were assigned to negative control group (without virus infection and without intervention), positive control group, or experiment group. In the positive control group and the experiment group, the HIV⁃1 89.6/TZM⁃bl model and HIV⁃1 89.6/MT⁃2 model were established by infecting HIV⁃1 89.6. After virus infection, 5 concentrations of phloretin or EGCG were immediately added to TZM⁃bl cells of the experiment group, and 5 concentrations of phloretin were immediately added to MT⁃2 cells of the experiment group. The relative virus levels in various groups were evaluated through detecting the expressions of luciferase reporter genes. Results (1) The relative activity of A549 cells of the experiment group was lower than that of the control group (P<0.05), namely, phloretin and EGCG had different kill and inhibitory effects on A549 cells. (2) The relative activities were all >80% in MT⁃2 cells of the experiment group via the intervention of 5 concentrations of phloretin. The relative activities were all >80% in TZM⁃bl cells of the experiment group via 1.25 μmol/L, 2.5 μmol/L of phloretin intervention. The relative activity was >80% in TZM⁃bl cells of the experiment group via 5 concentrations of EGCG intervention. (3) Compared with the positive control group, the relative virus level was declined in MT⁃2 cells supernate of the experiment group via 10 μmol/L and 20 μmol/L of phloretin intervention, the relative virus level was declined in TZM⁃bl cells of the experiment group via 5 μmol/L, 10 μmol/L, and 20 μmol/L of phloretin intervention, and the relative virus level was declined in TZM⁃bl cells of the experiment group via 5 concentrations of EGCG intervention (P<0.05). (4) The therapeutic index of phloretin in the HIV⁃1 89.6/MT⁃2 model and HIV⁃1 89.6/TZM⁃bl model was >2.064 and 2.078, respectively. The therapeutic index of EGCG in the HIV⁃1 89.6/TZM⁃bl model was >3.587. Conclusion Phloretin and EGCG may regulate N6⁃methyladenosine modification, so as to inhibit HIV⁃1 infection and replication in host cells through regulating METTL16 target in methyltransferase.