Background Hand, foot and mouth disease (HFMD) is a serious infectious disease, which has become a public health problem. Previous studies have shown that temperature may influence the incidence of HFMD, but most only focus on single city and the results are highly heterogeneous. Therefore, a multicity study was conducted to explore the association between temperature and HFMD in different cities and search for modifiers that influence the heterogeneity. Methods We collected daily cases of childhood HFMD (aged 0-5 years) and meteorological factors of 21 cities in Guangdong Province in the period of 2010-2013. Distributed lag non-linear model (DLNM) with quasi-Poisson was adopted to quantify the effects of temperature on HFMD in 21 cities. Then the effects of each city were pooled by multivariate meta-analysis to obtain the heterogeneity among 21 cities. Potential city-level factors were included in meta-regression to explore effect modifiers. Results A total of 1,048,574 childhood cases were included in this study. There was a great correlation between daily childhood HFMD cases and temperature in each city, which was non-linear and lagged. High heterogeneity was showed in the associations between temperature and HFMD in 21 cities. The pooled temperature-HFMD association was peaking at the 79th percentile of temperature with relative risk (RR) of 2.474(95%CI: 2.065-2.965) as compared to the median temperature. Latitude was the main modifier for reducing the heterogeneity to 69.28% revealed by meta-analysis. Conclusions There was a strong non-linear and lagged correlation between temperature and HFMD. Latitude was strongly associated with the relationship between temperature and HFMD. Meanwhile, it had an effect on modifying the relationship. These findings can conducive to local governments developing corresponding preventive measures.