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To date, there has been little research considering both autism spectrum disorder (ASD) symptom severity and motor impairment simultaneously when investigating their associations with obesity. This study was designed to identify the moderating role of symptom severity in the relationship between motor competence and overweight/obesity for children with ASD. Seventy-eight children with a clinical diagnosis were recruited from a large autism rehabilitation center in Wuhan, China. Chi-square, partial correlation, and moderation regression analyses revealed that the prevalence of overweight and obesity was similar regardless of symptom severity. Balance was the only motor skill that correlated with body mass index. Furthermore, symptom severity significantly moderated the correlation. Children with low autism severity might be more likely to demonstrate the relationship between balance and body mass index than those with high autism severity. Combating obesity by enhancing motor competence should cautiously consider personal and environment factors such as individual severity of ASD.