We studied the effects of habitat mosaics on butterfly assemblage on multiple spatial scales: landscape, landscape element, local habitat, and microhabitat, based on the transect counts conducted along a 3.84 km route. The transect route, including 21 local habitats, passed through two distinct areas: 1.65 km of a secondary deciduous Quercus forest and the grove of a shrine in Hiraoka, and 2.19 km of a mosaic of secondary deciduous Quercus forest, grassland, and farmland in Narukawa. The diversity of the landscape elements and species richness were higher in Narukawa than in Hiraoka; the landscape mosaic enhanced the species richness in Narukawa. However, the diversity indices and specialist species (univoltine tree feeder) were decreased in this mosaic landscape. The species richness at local habitats was also increased by the mosaic of microhabitats, such as the herbaceous layer, glade, and mantle in the local habitats, whereas it was decreased by an abundant shrub layer. The ratios of species richness to abundance in the local habitats were lower than expected based on random sampling from the total of Hiraoka and Narukawa. This means that local assemblages were non-random samples from an assemblage on the landscape or regional scale, and were made up by the process of habitat selection of butterfly species in the assemblages on the landscape or regional scale. For conservation of butterfly assemblages, we recommend that woodlands should be kept without fragmentation, but with glades or small grasslands, and with clearance of the shrub layer along the path.