Previous research has shown that training on inhibitory control (IC) leads to functional neural plastic changes, although this effect on individuals with different levels of IC abilities has yet to be studied. Here, we examined the individual differences in IC abilities of 85 participants, who performed a Simon task while undergoing a functional magnetic resonance imaging (fMRI) scan. Participants in the experimental group followed an 8-day training session on IC between the pre- and the post-test, whereas the control group did not receive any training. The fMRI results reported that, in comparison to the control group, the training session elicited different patterns of neural adaptation between participants with high- and low-IC abilities in the experimental group. While training reduced activation levels in the supplementary motor area (SMA), bilateral thalamus, and left anterior cingulate cortex (ACC) of individuals with low-IC performance prior to the training, the same pattern was not found in participants with high-IC performance. In addition, individual differences in IC abilities before training also positively correlated with activation reduction in these brain regions after training. These results suggest that individual differences in IC abilities modulate the neural plasticity of IC, and IC training specifically enhanced neural efficiency in individuals with low-IC abilities. Our findings provide a novel perspective for investigating the functional neuroplasticity of the IC system by highlighting the interaction between individual variances in IC abilities and short-term training effects.