Background: The aim of this study was to investigate the olfactory bulb (OB), fusiform gyrus (FG) and amygdala volumes and superior temporal sulcus (STS) and olfactory sulcus depths (OSD) using magnetic resonance imaging in children with autism spectrum disorders (ASDs) in comparison with those in typically developing (TD) controls and their effects on autism symptom severity. Methods: This study included 79 children with ASDs and 100 TD controls aged 4–10 years. The Childhood Autism Rating Scale (CARS) and Autism Behavior Checklist (AuBC) were used to measure ASD severity. Results: The ASD group had significantly lower OB, FG and amygdala (right, left and total) volumes and significantly higher right OSD than the TD group. However, no significant difference in STS depth was found between the groups. Left and total OB volumes and right, left and total OSD were positively correlated with AuBC use of body and objects use scores, while left and total OSD were negatively correlated with AuBC language skill scores. Right, left and total amygdala volumes were positively correlated with CARS scores and right FG volume was positively correlated with AuBC use of body and objects use scores. After controlling for potential confounders such as total brain volume, age and sex, the results of the analysis of covariance remained unchanged. FG volume was the strongest predictor of ASD in the multiple logistic regression model. Conclusions: This study suggests that OB, FG and amygdala volumes and right OSD may play a role in the etiopathogenesis of cortical development in children with ASD.