Post-windthrow management delays forest biomass recovery by altering the situation of disturbance legacies and can change the species composition. Although the short-term effects of post-windthrow management have been well studied, we do not have enough knowledge about the long-term effects of post-windthrow management on species composition and biomass recovery. Those effects associated with an increase in the windthrow frequency are also unknown. Although forest landscape models can effectively evaluate these effects, conventional models do not represent the regeneration process on downed logs, which is essential for simulating forest succession. We focused on hemiboreal forests in northern Japan and aimed to (1) incorporate the regeneration process on downed logs into LANDIS-II, which is one of the most used forest landscape models; (2) evaluate the long-term effects of post-windthrow management on tree species composition and aboveground biomass recovery; and (3) evaluate the associated long-term effects of interactions between post-windthrow management and increased windthrow frequency. We incorporated the regeneration process on downed logs into LANDIS-II by regulating the probability of the establishment of species that depend on dead wood, such as spruce, according to the availability of well-decayed dead wood. The incorporation of this process resulted in simulations of trends in species composition and aboveground biomass recovery after post-windthrow management that were more accurate than those produced by the original model. In the modified LANDIS-II simulation, reductions in dead wood and advanced seedlings due to salvage logging had little effect on the tree species composition or aboveground biomass recovery; however, the complete destruction of advanced seedlings by scarification induced a delay in aboveground biomass recovery and a shift to birch-dominated forests that continued for 100~years. In addition, the reduction in dead wood due to salvage logging decreased the number of seedlings, especially of dead wood-dependent species, that established after windthrow. When the windthrow frequency doubled, this decrease in seedlings induced a delay in aboveground biomass recovery, and a substantial decrease in dead wood-dependent species biomass occurred after a subsequent windthrow event. However, after the second windthrow event and following scarification, the forest recovered in the same way as after the first windthrow because the destruction of advanced seedlings and understory plants, namely, dwarf bamboo (Sasa spp.), by scarification reset the site conditions. To conserve the species composition and aboveground biomass of hemiboreal forests under climate change, which is expected to increase windthrow frequency, salvage logging and scarification should be avoided.