To understand the nutritional conditions of culled wild sika deer (Cervus nippon) and their suitability as a pet food component, we compared the ruminal community compositions of deer living in different food habitats (Nagano winter, Nagano spring, and Hokkaido winter) using next-generation sequencing. Twenty-nine sika deer were sampled. Alpha and beta diversity metrics determined via 16S and 18S ssrRNA amplicon-seq analysis showed compositional differences. Prevotella, Entodinium, and Piromyces were the dominant genera of bacteria, fungi and protozoa, respectively. Moreover, 66 bacterial taxa, 44 eukaryotic taxa, and 46 chloroplastic taxa were shown to differ significantly among the groups by linear discriminant analysis effect size (LEfSe). Total RNA-seq analysis showed 397 significantly differentially expressed transcripts (q < 0.05), of which 258 were correlated with bacterial amplicon-seq results (Pearson correlation coefficient > 0.7). The amplicon-seq results indicated that deciduous broadleaf trees and SAR were enriched in Nagano, whereas graminoids, Firmicutes and fungi were enriched in Hokkaido. The ruminal microbial community were corresponded with different food habits, related to the severe snow conditions in Hokkaido in winter and the richness of plants with leaves and acorns in Nagano winter and spring. These findings are useful for understanding the nutritional conditions of wild sika deer.