The presence of an intellectual disability (ID) alongside autism is considered to increase the risk for mental health and behavior problems in children and adolescents. Existing evidence is restricted by looking at ID as a categorical classification. The study aimed to examine the association of cognitive and adaptive behavior skills with internalizing and externalizing problems in a large sample of autistic children and adolescents, across a wide range of cognitive skills. Participants were 2759 children and adolescents aged between 4 and 18 years recruited as part of the Simons Simplex Collection (SSC), of whom 709 (approximately 25%) had ID. Multiple regression models examined associations of internalizing and externalizing problems with cognitive and adaptive skills (communication, daily living, and socialization skills). Cognitive skills were not associated with externalizing problems but were associated with more internalizing problems in autistic children without ID (Cog β: 0.126). All adaptive skill domains were inversely associated with externalizing (Communication β: -0.145; Daily-Living β: -0.132; Socialization β: -0.289) and internalizing problems (Communication β: -0.074; Daily-Living β: -0.064; Socialization β: -0.213) in those without ID. Daily living (β: -0.158) and socialization skills (β: -0.104) were inversely correlated with externalizing problems in autistic children with ID, while only socialization problems (β: -0.099) were associated with internalizing problems in this group. Socialization skills were systematically associated with internalizing and externalizing problems across all levels of cognitive functioning. Supporting social skills development may benefit all aspects of child mental health, while recognizing that children with higher cognitive skills are more vulnerable to internalizing problems might assist with earlier identification of these problems.