Background Type B influenza virus circulates every year with lower activity than that of influenza A virus in China. During 2017 to 2018 winter season, a sharp surge of influenza activity dominated by type B/Yamagata lineage virus caused unprecedented medical burden in Beijing. The research aimed to understand the underlying mechanism for this circulation and be prepared for epidemics in the future. Methods Sera samples collected from the patients in 2016-2017 and 2017-2018 flu seasons were tested for profiling hemagglutinin inhibition (HI) antibodies against both prevailing Victoria and Yamagata lineages of type B influenza viruses. Results It showed that the positivity of HI antibodies against both lineages of the virus in 2017-2018 winter was higher than that in 2016-2017, while no difference of the positivity of HI antibodies was observed between the two winter seasons. Meanwhile, significant elevated geometric mean titer (GMT) against both lineages of influenza B viruses was found in the specimens collected during 2017-2018 flu season than that from 2016-2017, suggesting the viruses might undergo antigenic changes. These results also suggested that lower GMT against both type B variants in 2016-2017 might serve as an immunological niche for the dominating of B/Yamagata virus in China during 2017-2018 winter season. Conclusions Our findings have implication that vaccines including both lineages of influenza B virus in formula might be a better preparation against influenza B epidemics.