Cross-sectional studies about the association between social integration, social exclusion, and vaccination behavior among internal migrants in China are lacking. In this study, we aimed to explore the association between the influenza vaccination behavior and social integration as well as social exclusion in China based on a cross-sectional study. We included 12,467 participants aged 15 years old or above from the 2017 Migrant Population Dynamic Monitoring Survey (MDMS). We used univariate analysis and logistic regression models to access the association between social integration, exclusion status, and influenza vaccination rates. Results suggested that the association between social integration and the vaccination rate was significantly positive. Moving between different districts impact on people’s mental health and their health performance. Significant association between influenza vaccination behavior and education attainment, income status, health record, and awareness of basic public health services program was reported. Therefore, in order to reduce the incidence of influenza disease and increase the vaccination rate, policymakers and the public should promote social integration for internal migrants. Meanwhile, our finding also implies possible strategies to promote COVID-19 vaccination.