Background In the long process of adaptive evolution, many small mammals engage in coprophagy, or the behavior of consuming feces, as a means to meet nutritional requirements when feeding on low-quality foods. In addition to nutritional benefits, coprophagy may also help herbivores retain necessary gut microbial diversity and function, which may have downstream physiological effects, such as maintaining energy balance and cognitive function. Here, we used collars to prevent Brandt’s vole (Lasiopodomys brandtii) from engaging in coprophagy and monitored changes in microbial community structure, energy metabolism, and memory formation. Results In this research, we found that coprophagy prevention decreased alpha diversity of the gut microbiota, and altered abundances of microbial taxa such as Bacteroidetes, Firmicutes and Oscillospira. The coprophagy prevention decreased body mass while increased food intake and ghrelin level in serum. Importantly, coprophagy prevention decreased vole’s memory and neurotransmitters in brain. The administration of acetate compensated for the energy loss and decline of spatial memory caused by coprophagy prevention and partially rescued the composition and structure of gut microbiota. Conclusions These findings identify relationship between coprophagy behavior and interactions between the gut microbiota, energy metabolism and neurological function. Our results suggest that coprophagy may have a positive effect on animal’s nutritional requirements and ecological adaptations by improving memory function.