Background: Inhibitory control is a higher-order cognitive function that affects children’s lives and learning, and the development of inhibitory control plays a vital role in the overall development of preschool children. However, most studies have paid more attention to inhibitory and physical fitness, but less focus on motor competence. Therefore, the purpose of this study was to explore the association between motor competence and inhibitory control in preschool children. Methods: A total of 160 preschool children aged 3 to 6 years were selected using a stratified random sampling method, and both motor ability and inhibitory control were assessed. Motor competence was assessed via the Children’s Motor Assessment Battery, Version 2 (MABC-2). Inhibitory control was assessed using the one-on-one iPad-based Early Year Toolbox and reflected by reaction time and accuracy. Results: A total of 153 preschoolers were included in the final statistical analysis. After adjusting the confounders, motor competence was associated with accuracy (β = 0.010, 95% CI: 0.003, 0.017). Similarly, a negative association was observed between motor competence and reaction time (β = −0.008, 95% CI: −0.014, −0.002). Compared with the participants in the lowest group, motor competence (β = 0.051 95% CI: 0.003, 0.098), manual dexterity (β = 0.106 95% CI: 0.043, 0.170), and balance (β = 0.065 95% CI: 0.002, 0.129) were all positively associated with accuracy of those in the highest group. Conclusions: A positive relationship between motor competence and the accuracy of inhibitory control was observed in preschoolers, whereas a negative relationship between motor competence and the reaction time of inhibitory control was also identified. Enhancing preschool children’s motor competence is likely to facilitate their development of inhibitory control.