Severe hand, foot, and mouth disease (HFMD) is likely to develop critical complications such as brainstem encephalitis, acute pulmonary edema, and circulatory failure, which cause child mortality during outbreaks. This study aims to investigate factors that predict the severity of HFMD. One hundred sixteen in-patient children with severe HFMD and 202 with mild HFMD were retrospectively enrolled. Potential factors were collected for each child including sex, age, residence, modes of delivery, birth weight, virus types causing HFMD, and virus exposure history. Univariate and multivariable logistic regression were used to determine which factors were associated with HFMD severity. In the univariate analysis, breastfeeding (OR 0.514, 95 % CI 0.309-0.856), rural residence (OR 1.971, 95 % CI 1.239-3.137), current Enterovirus 71 (EV71) infection (OR 2.539, 95 % CI 1.504-4.287), and previous Epstein-Barr virus (EBV) exposure (OR 3.136, 95 % CI 1.863-5.278) were each associated with the severity of HFMD. In the multivariate model, breastfeeding (OR 0.570, 95 % CI 0.332-0.980), rural residence (OR 1.973, 95 % CI 1.202-3.237), current EV71 infection (OR 2.290, 95 % CI 1.315-3.987), and previous EBV exposure (OR 2.550, 95 % CI 1.470-4.422) remained independently associated with the severity of HFMD. In conclusion, previous EBV exposure, EV71 infection, and rural residence are risk factors for severe HFMD; breastfeeding is a protective factor.