A rapid, sensitive and simple microflow cytometry-based agglutination immunoassay (MCIA) was developed for point-of-care (POC) quantitative detection of SARS-CoV-2 IgM and IgG antibodies. The antibody concentration was determined by using the transit time of beads aggregates. A linear relationship was established between the average transit time and the concentration of SARS-CoV-2 IgM and IgG, respectively. The limit of detection (LOD) of SARS-CoV-2 IgM and IgG by the MCIA measurement are 0.06 mg/L and 0.10 mg/L, respectively. The 10 µL sample consumption, 30 min assay time and the compact setup make this technique suitable for POC quantitative detection of SARS-CoV-2 antibodies.