Objective: This study aims to investigate the epidemiological distribution of HFMD and quantify the association of temperature with the incidence of children’s HFMD in Nanjing, China. Methods: Daily counts of HFMD in children under 5 years and daily meteorological variables during 2011-2016 were obtained. Descriptive statistics were used to describe the epidemiological characteristics and distributed lag non linear model (DLNM) was used to assess the associations of temperature on HFMD cases. Results: A total of 104 977 HFMD cases aged 0-5 years were reported in Nanjing during the study period and the male to female sex ratio was 1.49∶1. The average annual incidence was 213.5 per 100 000. A bimodal seasonal pattern was observed and the south and west were found to be the high incidence areas in the city. Of these laboratory confirmed enteroviruses positive cases, 32.5% cases were positive for EV-A71 infections, 29.1% cases were positive for CV-A16 infections and 38.4% cases were positive of other enteroviruses infections. The temperature HFMD relationships were non linear and showed obvious lag effects. The cumulative relative risk presented as an approximately inverted U shape over 14 days and peaked at 25.7 ℃ with value of 2.71(95%CI=1.93-3.81). Subgroup analyses revealed that males and children aged <1 year were more vulnerable to temperature variations. Conclusion Epidemiological characteristics of HFMD among children aged 0-5 years old in Nanjing presented temporal and regional distribution. The temperature has significant impact on children’s HFMD occurrence.