Coronavirus disease 2019 (COVID-19) emergence in late 2019, and wide spread quickly in the world. In China, the COVID-19 epidemic situation entered a low level now. With the arrival of flu season, the number of patients with respiratory symptoms is increasing. We reported three cases of patients who co-infected with SARS-CoV-2 and influenza A virus (IAV), and they were all treated with nirmatrelvir-ritonavir (NMV/r) and baloxavir marboxil. Due to the overlapping clinical features between the two diseases, it is important to identified them and gave the antiviral therapy timely.