We retrospectively analyzed serum IgM antibodies (Abs) to influenza viruses from two tertiary hospitals in Beijing from December 2016 to February 2018. Samples from 36,792 patients, aged 0-98 years, were collected and tested. Among the patients, 923 children from two winter flu seasons were assayed with both antigens and IgM Abs to Flu A and Flu B and assigned as paired groups. Another 2,340 adults and 1,978 children with only antigen tested in the 2016 and 2017 winter flu seasons were named as unpaired groups. IgM Abs-positivity rates in children were 0.80% and 36.57% for Flu A and Flu B, respectively, peaking at 4-5 years of age. For adults, the Flu A and Flu B IgM Abs-positivity rates were 10.34% and 21.49%, respectively, peaking at 18-35 years of age. The trend of temporal distribution between the children and the adults was significantly correlated for IgM Abs to Flu B, but not for Flu A. Compared with unpaired groups, the detection rate of Flu A antigen was significantly higher than IgM Abs in children, whereas frequencies of IgM Abs were higher than antigen in adults. Incidence of Flu B antigen was sharply increased in 2017 winter than in the 2016 winter in both children and adults, but no concomitant increase was observed in IgM Abs to Flu B. For paired children groups, incidence of Flu B antigen in the 2017 flu season was significantly higher than that in the 2016 flu season; in contrast, positive rates of IgM Abs in the 2017 flu season were even lower than those in 2016. Considering antigen detection may reflect the Flu A/Flu B epidemic, our results indicate single-assayed IgM Abs were less effective in the diagnosis of acute influenza virus infection, and the use of this assay for epidemiology evaluations was not supported by these findings.