Many studies have reported abnormalities in the volume of subcortical structures in individuals with autism spectrum disorder (ASD), and many of these change with age. However, most studies that have investigated subcortical structures were cross-sectional and did not accurately segment the subcortical structures. In this study, we used volBrain, an automatic and reliable quantitative analysis tool, and a longitudinal design to examine developmental changes in the volume of subcortical structures in ASD, and quantified the relation between subcortical volume development and clinical correlates. Nineteen individuals with ASD (16 males; age: 12.53 ± 2.34 years at baseline; interval: 2.33 years) and 14 typically developing controls (TDC; 12 males; age: 13.50 ± 1.77 years at baseline; interval: 2.31 years) underwent T1-weighted MRI at two time points. Bilaterally, hippocampus volume increased from baseline to follow-up in both ASD and TDC, with no difference between groups. Left caudate and right thalamus volume decreased in ASD, but did not change in TDC. The decreases in left caudate and right thalamus volume were related to ASD social score. Right amygdala volume was larger in ASD than in TDC at baseline but not at follow-up. These results confirm previous cross-sectional findings regarding the development of subcortical structures in ASD. The association between developmental changes in left caudate and right thalamus volume and ASD social score offers an explanation for the social deficits in ASD. Results also captured the different abnormality of amygdala volume between childhood and late adolescence.