Hand, foot and mouth disease (HFMD) is an infectious disease that affects mostly children. The children with HFMD also have other immune and metabolic disorders. However, the association of these disorders with the severity of HFMD has not yet been determined. In this study, we used a case-control study design to examine the correlation of immune and metabolic disorders with HFMD development in children. 406 mild and severe patients were recruited and divided into different subgroups based on the number of days from the initial onset time to hospitalization (1, 2, 3, 4, and ≥5 days). Logistic regression model was used to define the predictors of severe HFMD. We found that the patients from rural area (OR = 1.76, 95% CI [1.19~2.63], P = 0.005) or with body temperature of >39°C (OR = 2.14, 95% CI [1.12~4.12], P = 0.022) exhibited higher risk for severe symptoms. In addition, the risk increased with the rise of body temperature by using a Chis-quare trend test (P = 0.01). We also found that a decreased number of eosinophils was an predictor of severe HFMD at 1, 2, 3,and 4 days post infection (dpi). Decreased levels of Na+, Cl-, and creatine kinase were also predictors at 1 and ≥5 dpi. On the other hand, elevated level of globulin was a predictor for severe HFMD at 4 dpi and ≥5 dpi, and the increased number of neutrophils or increased level of alkaline phosphatase posed risk for severe HFMD at 3 and ≥5 dpi. Our results suggested that rural living, hyperpyrexia, changes in the immune system that include the numbers of eosinophils and neutrophils and the levels of IgG and globulin, and metabolic alterations, such as the levels of alkaline phosphatase, Na+, Cl-, and creatine kinase in peripheral blood are predictors of severe HFMD.