The Child Behavior Checklist 1.5–5 (CBCL 1.5–5) is applied to identify emotional and behavioral problems on children with developmental disabilities (e.g., autism spectrum disorder [ASD] and developmental delays [DD]). To understand whether there are variations between these two groups on CBCL DSM-oriented scales, we took two invariance analyses on 443 children (228 children with ASD). The first analysis used measurement invariance and multiple-group factor analysis on the test structure. The second analysis used item-level analysis, i.e., differential item functioning (DIF), to discover whether group memberships responded differently on some items even though underlying trait levels were the same. It was discovered that, on the test structure, the Anxiety Problems scale did not achieve metric invariance. The other scales achieved metric invariance; DIF analyses further revealed that there were items that functioned differently across subscales. These DIF items were mostly about children’s reactions to the surrounding environment. Our findings provide implications for clinicians to use CBCL DSM-oriented scales on differentiating children with ASD and children with DD. In addition, researchers need to be mindful about how items were responded differently, even though there were no mean differences on the surface.