How species diversify in highly fragmented landscapes while maintaining genetic connectivity remains a central question in evolutionary biology. The megascolecid earthworm Amynthas aspergillum exemplifies this paradox, showing deeply divergent mitochondrial lineages despite extensive nuclear gene flow across southern China. We conducted whole-genome resequencing across its core distribution in the Guangxi karst region to elucidate the population structure and processes underlying this cytonuclear discordance. Genome-wide analyses identified three genetically distinct groups shaped by fine-scale karst isolation, alongside pervasive historical and contemporary introgression. Demographic modeling revealed rapid diversification during the Late Pleistocene (~0.14 Ma) with pronounced fluctuations in effective population size. Although isolation increased inbreeding and mutational load in some lineages, introgression persisted even among deeply divergent mitochondrial clades. Notably, several introgressed regions showed strong signatures of positive selection, including genes involved in mitochondrial function and metabolism. Together, these results demonstrate that gene flow can simultaneously mitigate the genomic costs of isolation and promote functional innovation via adaptive introgression, providing a genomic framework for diversification with gene flow in subterranean invertebrates inhabiting fragmented karst landscapes.