The implications of migration for gut microbial community composition and function, and effects on population health of host animals are poorly known. In this study, we quantified migration patterns and gene flow for moose populations in northeast China and tested their relationships to recent climate warming. And we then characterized moose gut microbial composition and tested its relationships to moose migration patterns. We found that moose populations increasingly moved northward or to higher latitude due to late spring warming. Migratory and isolated moose populations differed in their gut microbe composition and frequency of different functional groups of bacteria that relate to digestion and diet composition. Gut microbe composition was also related to different environmental variables in isolated vs. migratory moose populations. Our results suggested that gut microbes of isolated moose populations were only related to altitude, whereas those in migratory moose populations were related to temperature, precipitation, longitude and latitude. We believe that differences in the taxonomic and functional composition of gut microbiota relating to digestion are adaptive. Consequently, this study highlights that special attention should be placed on isolated populations of moose, and ecological corridors or translocation of individuals may be needed for moose conservation to allow persistence in the face of global warming.