Objective: To analyze the epidemic characteristics of hand, foot and mouth disease (HFMD) in Beijing and explore the short-term lag effect of daily average temperature on HFMD. Methods: The incidence data and meteorological data of HFMD were collected from Xicheng District, Chaoyang District, and Changping District of Beijing between January 2009 and December 2018. The dose-response relationship and short-term lag effect of temperature and HFMD incidence were explored by the distributed lag non-linear model (DNLM). Results: From 2009 to 2018, a total of 97 210 cases of HFMD were confirmed in Xicheng District, Chaoyang District, and Changping District of Beijing. The incidence rate of HFMD in Xicheng district was 71.83/100 000, which was the lowest in three districts. The total annual average incidence was 146.89/100 000 in the three districts. The cases were concentrated from May to July, with a small peak in October to November. The ratio of male to female was 1.49∶1, and the median age of the patients was 3.08 (1.89, 4.39) years old, which showed a decreasing trend in children under 6 years old (Z=-30.11, P<0.01). The DNLM showed that the cumulative relative risk (RR) curve had a bimodal distribution, with RR of 1.36 (95%CI: 1.05-1.76) and 1.35 (95%CI: 1.10-1.66), and the peak values appeared at 4 ℃ and 26 ℃, respectively. Conclusions: The incidence rate of HFMD in Xicheng was the lowest in three districts of Beijing. In addition, the incidence of HFMD is seasonal, and the incidence is higher in spring and summer than that in autumn and winter. Daily average temperature had a lag effect on HFMD, which was different between high temperature and low temperature.