We aimed to investigate the structural neuroplasticity associated with different levels of sports experience and its effect on the corresponding resting-state functional circuitry. We recruited 18 skilled baseball batters (SB), 19 intermediate baseball batters (IB), and 17 healthy controls (HC), and used magnetic resonance imaging methods to compare their regional gray-matter volume (GMV) and seed-based resting-state functional connectivity (rsFC). Our results revealed that a quadratic function could better depict intergroup differences in regional GMV than a linear function. In particular, the IB showed lower or higher regional GMV than the other two groups. The difference in GMV in the supplementary motor area and areas belonging to the ventral stream, including the middle temporal gyrus and middle temporal pole, might be possibly related to baseball-specific motor and perceptual experience, such as inhibitory action control and pitch identification. On the other hand, the stronger rsFC seeded from the right middle temporal pole to the default mode network, particularly in the precuneus, in the SB and IB relative to that in the HC might be possibly associated with the theory of mind, such as deciding whether to swing or not against the pitcher by detecting the spatial information of pitches. In conclusion, our three-group design enabled the capture of the unique and transient changes that occur during the intermediate phase of expertise development. Our findings indicated that structural and functional brain changes do not necessarily linearly increase as a function of experience as previously suggested by the literature.