The aim of this study was to investigate the level of inactivated A71 (EV-A71) vaccination in Pudong New Area of Shanghai and its effects on the epidemiology and pathogen spectrum of hand–foot–mouth disease (HFMD) in this area, as well as to provide a basis for improving the prevention and control strategy of HFMD in this area. Data were collected from the “Comprehensive Management Cloud Platform for Immunization Program” system from December 2016 to December 2022. The data on HFMD cases from January 2012 to December 2022 were extracted from the “China Information System for Disease Control and Prevention”. A total of 484,056 doses were administered. The vaccination rate of the first dose was 14.03%, and the full vaccination rate was 13.33%. There were significant differences between the first dose and the full vaccination rate in different years (χ2 = 46,538.831, p < 0.001, χ2 = 50,013.946, p < 0.001). A total of 91625 cases of HFMD were reported, including 58 severe cases, and no deaths. Before and after the administration of the inactivated EV-A71 vaccine, there were statistical differences in the distribution of HFMD cases in terms of gender, household registration, occupation, and age (p < 0.001). The etiological surveillance results showed that the rate of enterovirus positivity was 84.15%, with 9.85% being EV-A71, 23.74% CV-A16, and 50.56% non-EV-A71 and non-CV-A16. The coverage rate of the inactivated EV-A71 vaccine in Pudong New Area was not high, and the incidence of HFMD showed a downward trend after the postmarketing of the vaccine. The majority of HFMD infections were non-EV-A71 and non-CV-A16, with CV-A6 accounting for the highest proportion. It is recommended to accelerate the development of combined vaccines to provide more antibody protection.