How marine organisms achieve connectivity across highly fragmented deep-sea hydrothermal vents remains a fundamental question in evolutionary biology. While broad biogeographic patterns are documented, the interacting roles of bathymetry, ocean currents, and historical climate fluctuations in shaping intraspecific divergence remain largely elusive. The deep-sea hot vent endemic polychaete Paralvinella cf. hessleri, distributed across the Western Pacific, provides an opportunity to decode these complex dispersal mechanisms. Here, we present a comprehensive population genomic study of this species, analyzing 160 individuals across 12 well-separated hydrothermal vents covering Okinawa Trough, Izu-Ogasawara Arc and Mariana Arc. Surprisingly, substrate type, rather than geographic distance, drives primary population divergence. Extreme geochemical differences, notably pH and heavy metals, sharply isolate sediment-hosted Okinawa Trough populations from bare-rock Izu-Ogasawara and Mariana lineages. Regionally within the Okinawa Trough, the Kuroshio Current system drives asymmetric gene flow, while bathymetry strictly stratifies populations: deep vents (>1,000 m) maintain a massive panmictic gene pool, whereas shallow sites (~600 m) exhibit strong local adaptation. By untangling the synergistic effects of substrate heterogeneity, ocean currents, and depth on deep-sea diversification, our findings provide critical baselines for benthic conservation in the face of increasing anthropogenic impacts.