Purpose: Although previous studies have found an association between brain iron levels and brain function, few have explored this relationship in children with autism spectrum disorder (ASD). Thus, we aimed to determine the association between quantitative susceptibility mapping (QSM)-derived magnetic susceptibility values (MSVs) and brain function in children with ASD. Materials and Methods: The study included children with ASD who underwent both a brain magnetic resonance imaging with QSM and the Wechsler intelligence scale for children intelligence quotient (IQ) test. Select subcortical brain regions (caudate, putamen, globus pallidus, and thalamus; both right and left) were automatically segmented, and the MSVs were extracted from the QSM. The IQ score parameters (verbal comprehension, working memory, perceptual organization, and processing speed indices, and full-scale IQ) were measured. Correlation analysis was used to assess the association between age and IQ test parameters and between age and MSV. Linear regression analysis was performed to measure the relationship between the MSV and IQ test parameters. Results: A total of 23 children with ASD (median age [interquartile range]: 10 [8–14] years; 12 males) were included. Age was not correlated with any of the IQ test parameters (p > 0.05). There was a significant correlation between age and right-thalamus MSV (r = 0.443, p = 0.03); however, no such correlation was found with the MSVs of other regions (p > 0.05). Among the IQ test parameters, the verbal comprehension index significantly correlated with the left-caudate MSV (r = 0.420, p = 0.046) and the perceptual organization index significantly correlated with the right-globus-pallidus MSV (r = 0.414, p = 0.049). Conclusion Select subcortical MSVs were associated with IQ test parameters in children with ASD, suggesting that QSM is a potential neurodevelopmental marker.