Effortful control (EC) is a base of individuality in cognition and psychological adjustment. EC is defined as a capacity to control responses and behaviors. We investigated associations between individual differences of EC and regional gray and white matter volume (rGMV/rGMV) in 374 men and 306 women (age, 20.61 ± 1.82 years) using Japanese version of Effortful control scale (J-ECS). J-ECS consists of three subscales such as inhibitory control (IC), activation control (ACTC), and attentional control (ATC). Results showed that (a) IC was associated with larger rGMV in the dorsal part of anterior cingulate cortex (dACC), the supplementary motor area (SMA) and the pre SMA and larger rWMV in the dACC, (b) ACTC was correlated with smaller rGMV in the insula and the putamen, and (c) ATC was associated with larger rWMV in the inferior frontal gyrus, orbital frontal gyrus, ACC, and insula. Our study revealed key neuroanatomical correlations between EC and rGMV and rWMV.