A stage structures (scattered and school children) model with temperature-dependent latent period to investigate hand, foot and mouth disease (HFMD) transmission is proposed. The periodic delay induced by latent period in modelling brings new challenges to dynamics analysis. With the help of defined basic reproduction number $R_0,$ we prove: when $R_0<1,$ the disease-free equilibrium is globally attractive; when $R_0>1,$ this model is uniformly persistent. Next, the model is applied to simulate the HFMD reported data in Guangxi province, China from January 2018 to December 2019. The simulation results are consistent with our theories, and it also shows that scattered children are the main affected population. Finally, by comparing with time-averaged latent period, numerical experiments analyze the effect of time-varying latent period on HFMD transmission. Based on the HFMD transmission case in Guangxi Province, we find that the use of time-averaged latent period underestimates the real value of $R_0$ and the number of new infections containing scattered and school children is also underestimated.