
Japan relies heavily on foreign energy imports while hosting immense untapped geothermal resources. Leveraging domestic deep geothermal energy could mitigate import dependencies, alleviate land-use constraints, and provide stable base-load clean power. This study introduces major open-source enhancements to the energy system modeling framework PyPSA-Earth by integrating spatially explicit Enhanced Geothermal Systems (EGS) potentials and maritime hydrogen import routes across ten aggregated regional nodes for Japan’s 2050 net-zero transition. Through a co-optimized capacity expansion and dispatch framework across the power, heating, transport, and hydrogen sectors, results demonstrate that EGS plays a pivotal structural role as a continuous base-load source. Deploying 35.0 GW_el of EGS (capturing 21.3% of total power generation) significantly reduces the required expansion of land-intensive variable renewables—avoiding 104 GW of utility PV and 26 GW of onshore wind—and cuts stationary battery storage discharge capacity needs by 70.4% (-45.3 GW). Although geographically concentrated EGS in Kyushu increases inter-regional AC transmission grid expansion costs, net annual system costs decline by 6.1% (yielding net annual savings of €4.29 billion/a). In urban district heating, direct geothermal heat achieves a dominant 67.3% share (3.5 TWh/a). Regarding clean hydrogen, maritime imports dominate at 80.4% under the baseline CIF target (€1.49/kg H2). However, an import price increase to €2.24/kg H2 triggers a sharp structural shift: imports collapse to 1.9 TWh/a, shifting supply to domestic SMR with carbon capture and co-located EGS-electrolysis. These quantitative insights highlight deep geothermal energy as a crucial, land-saving domestic anchor for island energy transitions.