Background: Guangdong Province started the enterovirus A71 (EV71) vaccination campaign officially in August 2016. This study aimed to evaluate the effectiveness of the EV71 vaccine against EV71, CA16, CA6, or other enterovirus infection through post-marketing surveillance in Guangdong Province in 2017. Methods: A test-negative case–control design nested in a population-based cohort was used in this study. There were 3020 laboratory-confirmed child cases of hand, foot, and mouth disease (HFMD), including 409 children infected with EV71 and 2611 with CA16, CA6, or other enteroviruses. A total of 603 test-negative controls who were clinically diagnosed with HFMD in the same hospitals were enrolled in this study. Results: Of all the subjects, 383 (10.6%) had received two doses of the EV71 vaccine. Only one (0.2%) out of the 409 cases with EV71 was vaccinated. In addition, 137 (5.2%) out of 2611 cases with CA16, CA6, or other enteroviruses and 21 (3.5%) out of 603 negative controls were also vaccinated. The adjusted estimate of the effectiveness was 93.6% (95% CI: 51.0%, 99.2%; p<0.001) for cases with EV71. The protective effect of the EV71 vaccine for cases with CA16, CA6, or other enteroviruses did not reach significance (95% CI: -130.4%, 10.6%; p=0.134). Conclusion: The EV71 vaccine demonstrated very high protection against EV71 infection conferred by two doses of the EV71 inactivated vaccine used in Guangdong Province during 2017. No protection was found against CA16, CA6, or other enterovirus infections. Further development of combined vaccine options for HFMD control is needed.