Isovaleric acidemia is a metabolic disorder which disrupts normal metabolism of leucine due to the elimination of activity of isovaleryl-CoA dehydrogenase. Therefore, isovaleric acid and related metabolites accumulate in the body of patients. Because the treatment consists of dietary protein restriction, the percentage of carbohydrates in nutrition intake increases to maintain adequate calories to avoid metabolic imbalance. Thus, we need to pay more attention to the management and prevention of dental caries. In addition, dehydration and metabolic acidosis would happen when the patients are challenged with pressure or when they are sick, behavior management is a major concern when treating the patients with this disease. This case report presents a treatment of a 5-year-3-month-old boy who suffered from various dental caries in his mouth, diagnosed with early childhood caries, and under multiple dental visits, we have efficiently controlled the infection of dental caries and reestablished the occlusion of the patient.