Ohdaigahara has one of the largest natural forests in western Japan. The forest, however, is facing collapse because high densities of sika deer strip tree bark and browse on tree seedlings. The Ministry of the Environment has selected the forest in this area for restoration. In the Fagus crenata Blume-Abies homolepis Sieb. et Zucc.-Sasa nipponica Makino et Shibata community, one of the three main vegetation communities in Ohadaigahara, we conducted field experiments with manipulations of Sasa nipponica deer, mice and/or birds. The soil, plant and animal communities have been monitored since 1997. We also compared vegetation and bird communities among sites with different densities of deer. We found that the population of sika deer and the aboveground biomass of Sasa nipponica are currently in equilibrium, with a balance of supply and demand. In deer exclosures, however, the aboveground biomass of Sasa nipponica showed an eight-fold increase over a five-year period. A system dynamics model was constructed for deer-Sasa nipponica-soil interactions within the nitrogen cycle. In addition, the model included the effects of deer density and Sasa nipponica biomass on the number and diversity of tree seedlings, arthropods and birds. With the aim of promoting forest regeneration and an increase in ecosystem biodiversity, we determined the best management strategy for the deer population and Sasa nipponica biomass. We concluded that the aboveground biomass of Sasa nipponica must be reduced, along with a removal of deer, to prevent a rapid increase of Sasa nipponica biomass inhibiting the survival of tree seedlings. We also found that there is no optimal deer density or Sasa nipponica biomass, because they have different effects on different groups of organisms. Based on the model predictions, we present various proposals for restoring the Ohdaigahara forest.