Understanding the influence of temperature on hand-foot-and-mouth disease (HFMD) is an important public health concern as well as being a major climate-infection issue in mainland China. City-scale data of incidence rates (IRs) of HFMD and temperature from 2008 to 2009 in mainland China has been analyzed. There were two peak periods for HFMD prevalence from April to July and August to November. Regions with higher monthly IR of HFMD periodically shifted following the pattern of south-north-south from March to December. Monthly IR of HFMD at city scale were closely associated with both average monthly temperature and monthly temperature range. Our study shows that spatiotemporal trends of HFMD infection were sensitive to temperature variation, and suggest that preventive measures should be considered for limiting the epidemic of HFMD in the cities with higher monthly IR during the peak periods.