Carrying capacity is 1 driver of wildlife population dynamics. Although in previous studies carrying capacity was considered to be a fixed entity, it may differ among locations due to environmental variation. The factors underlying variability in carrying capacity, however, have rarely been examined. Here, we investigated spatial heterogeneity in the carrying capacity of Japanese sika deer (Cervus nippon) from 2005 to 2014 in Yamanashi Prefecture, central Japan (mesh with grid cells of 5.5 x 4.6 km) by state-space modeling. Both carrying capacity and density dependence differed greatly among cells. Estimated carrying capacities ranged from 1.34 to 98.4 deer/km². According to estimated population dynamics, grid cells with larger proportions of artificial grassland and deciduous forest were subject to lower density dependence and higher carrying capacity. We conclude that population dynamics of ungulates may vary spatially through spatial variation in carrying capacity and that the density level for controlling ungulate abundance should be based on the current density level relative to the carrying capacity for each area.