Habitat structure in Oku-Nikko, Japan, has been substantially modified by the overabundance of sika deer (Cervus nippon). A deer-proof fence (15.0 km and 900 ha) was constructed in 2001 to conserve vegetation. Although the understory inside the fence is dominated by Sasa nipponica (hereafter, Sasa), an important forage plant for deer, that outside the fence is dominated by Aster ageratoides leiophyllus (hereafter, Aster), an unpalatable plant to deer, and, partly, by bare floor. In this study, we examined the effects of deer on ground-dwelling insects and earthworms, the primary food resources of raccoon dogs (Nyctereutes procyonoides), and, thus, the bottom-up cascading effects of the herbivore on the omnivorous carnivore. Between July and September 2008, we examined the abundance of insects and earthworms by pitfall trapping and hand-sorting methods, respectively, both inside and outside the fence. The abundance of earthworms and insects (Scarabaeidae and Rhaphidophoridae) was higher on forest floors with Aster and/or bare floors outside the fence than on those with Sasa inside the fence. These results indicate that the increasing deer population in this area probably increased the number of these invertebrates outside the fence by modifying understory vegetation and/or depositing dung. Furthermore, the sighting rates of raccoon dogs obtained by spotlight counts were greater outside than inside the fence, suggesting that deer probably exert bottom-up cascading effects on raccoon dogs, at least during May to November, when the invertebrates are predominantly fed on by the omnivorous carnivore.