A multi-layer repository concept is proposed as an alternative to the single-layer repository concept to improve the disposal density of high-level radioactive waste (HLW) in Korea. Numerical simulations are performed to compare the coupled thermo-hydro-mechanical (THM) behavior in the existing Korean reference HLW disposal system (KRS) based on the single-layer repository concept to that in the new multi-layer repository concept. The applicability of the multi-layer repository concept, such as double- and triple-layer repositories, for the disposal of HLW is analyzed with respect to a maximum temperature criterion of 100 °C, evolution of saturation and pore pressure, and mechanical stability. Maximum temperatures are below 100 °C in the double- and triple-layer repository concepts, as in the single-layer reference, although two peaks in simulated temperatures are observed during the evolution of the thermal pulse, resulting from superposition of decay heat at different vertical levels in the multi-layer repository concept. There is no significant difference in the evolution of pore pressure and saturation among the three concepts. The evolutions of mean effective stress at the bentonite blocks and backfill materials are also not significantly different between the single-, double-, and triple-layer repository concepts, because the hydraulic behavior is quite similar, resulting in almost the same change in swelling pressure. Stress states in the rock mass near the tunnels and deposition holes remain below the Mohr-Coulomb failure envelopes at the repositories of 500 m depth in the single-, double-, and triple-layer repository concept simulations. However, the stress states exceed the Mohr-Coulomb failure envelopes at the repositories below 500 m depth (beneath the top layer) in the double- and triple-layer repository concepts. Also, mechanical analysis shows high potential for spalling failure around the deposition holes and tunnel roof in the double- and triple-layer repository concepts. Subsidence in the double- and triple-layer concepts due to the construction of repositories is much deeper than that in the single-layer concept, and uplift induced by heating the rock mass due to the decay heat in the double- and triple-layer concepts is much higher than in the single-layer concept. These results indicate that multi-layer repositories with larger depth intervals between layers are a feasible alternative to the KRS to safely achieve higher disposal density.