Abstract: Objective To analyze the epidemiological characteristics and the temporal-spatial distribution of severe cases of hand foot and mouth disease (HFMD) in Inner Mongolia from 2009 to 2016,and determine the key area, time and groups for the prevention and control and reduce the occurrence of severe cases. Methods Data collected from surveillance information of severe cases of HFMD in Inner Mongolia during 2009 to 2016 was analyzed. Results The incidence rate of severe HFMD cases was increased at first and then decreased, the peak value appeared in 2011. The severe cases of HFMD mainly occurred in children aged ≤ 3 years old, among which scattered children were at high risk. Males were more susceptible to severe HFMD than females in children aged ≤ 3 year old. The incidence peak of severe cases of HFMD appeared in 6-7 in the study years. A total of 1 278 cases were reported in Inner Mongolia from 2009 to 2016, with all annual incidence of 50.70 per l00 0000, accounting for 0.78% of the total. EV71 was major pathogens in severe cases of HFMD. The temporal and spatial clustering existed among the severe HFMD cases. The temporal dimension of HFMD was from May to July each year. The spatial dimension mainly distributed in the middle and south-west regions of Inner Mongolia. Conclusions Temporal and spatial clustering areas of severe HFMD were presented in this study. The incidence intensity varied obviously with region, which might be due to the climate factor. More attention should be paid to young children who have a high risk of severe HFMD to reduce disease incidence and strengthen the prevention and control of HFMD.