The physiological adaptive regulation of healthy population with a high fitness level is associated with enhanced cognitive control in brain. This study further investigated the effects of different levels of sporting experience on intrinsic brain networks involved in central autonomic processing using resting-state functional magnetic resonance imaging. We explored functional connectivity of four core regions within central autonomic network (CAN), namely posterior midcingulate cortex (pMCC), left amygdala (AMYG), and right anterior (aINS) and left posterior insular cortices, in advanced and intermediate baseball players, and compared their strength of connectivity with individuals without baseball-playing experience. Functional connectivity maps across three groups confirmed a close relationship between CAN and large-scale brain networks in sensory, motor and cognitive domains. Crucially, both advanced and intermediate batters demonstrated enhanced connectivity between pMCC and sensorimotor network, between right aINS and dorsal anterior cingulate cortex, and between left AMYG and right putamen, than controls. These results reflected a stronger interregional coupling in sensorimotor and cognitive control, and in motor skill consolidation. In conclusion, we provided evidence that different levels of sporting experience could reorganize/enhance intrinsic functional connectivity for central autonomic processing.