Hand-foot-mouth disease (HFMD) is primarily caused by enterovirus 71 and coxsackieviruses A16, and usually transmitted among children under five years old. HFMD has been a significant public health challenge in China. In 2015, there were 1767931 cases and 114 deaths reported in China. To understand the transmission of the disease, we examined the age-specific force of infection (FOI) and the transmission rate of HFMD in Chongqing using data from May 2008 to December 2011. Chongqing is the only municipality in the southwest part of China. It has the largest population density compared with other cities in the area, and its has a typical seasonality pattern of HFMD that was found in the southeastern part of China. The FOI of HFMD for Chongqing might be different between age groups, because we had an observation that the FOI of HFMD was identical among age groups before the 2008 outbreak, but was heterogeneity after the outbreak in Fuyang, Anhui Province. Regard to the transmission rate, we studied whether it changed during the year and studied the possible connection of changing in transmission rate with school closure and with holidays. Data of HFMD reported cases were obtained from the Data-center of China Public Health Science; demography data and meteorological data were obtained from the National Bureau of Statistics of China. We used catalytic model to estimate the age-specific FOI of HFMD for Chongqing, and used Time Series Susceptible Infectious Recovered (TSIR) model to estimate the time varied transmission rate of HFMD. In the TSIR model, the serial interval was assumed to be two weeks based on the fact that the incubation period of HFMD was 3–5 days and the infectious period was about 7–10 days. We calculated the proportion of HFMD incidence for each age group. Our results show that: the incidence of HFMD in Chongqing had two peaks, one in spring and one in winter; proportion of cases among children under six years old were 93%, with the largest fraction of cases among 2–3 years old; the FOIs in different age groups were different, FOI of 3–4 years old age group was the highest, and FOI of 35–39 years old was relatively higher than that of other adults; transmission rate among individuals changed during the year; transmission rate increased during summer and winter vocations, meaning that in China the transmission rate of HFMD in community was higher than the transmission rate in school. Control measures of HFMD should focus on young children, especially 3–4 years old, in community during summer and winter vocations.