One major characteristic of experts is intuitive judgment, which is an automatic process whereby patterns stored in memory through long-term training are recognized. Indeed, long-term training may influence brain structure and function. A recent study revealed that chess experts at rest showed differences in structure and functional connectivity (FC) in the head of caudate, which is associated with rapid best next-move generation. However, less is known about the structure and function of the brains of Baduk experts (BEs) compared with those of experts in other strategy games. Therefore, we performed voxel-based morphometry (VBM) and FC analyses in BEs to investigate structural brain differences and to clarify the influence of these differences on functional interactions. We also conducted graph theoretical analysis (GTA) to explore the topological organization of whole-brain functional networks. Compared to novices, BEs exhibited decreased and increased gray matter volume (GMV) in the amygdala and nucleus accumbens (NA), respectively. We also found increased FC between the amygdala and medial orbitofrontal cortex (mOFC) and decreased FC between the NA and medial prefrontal cortex (mPFC). Further GTA revealed differences in measures of the integration of the network and in the regional nodal characteristics of various brain regions activated during Baduk. This study provides evidence for structural and functional differences as well as altered topological organization of the whole-brain functional networks in BEs. Our findings also offer novel suggestions about the cognitive mechanisms behind Baduk expertise, which involves intuitive decision-making mediated by somatic marker circuitry and visuospatial processing.