In numerous animals, the vomeronasal organ (VNO) is a crucial chemosensory organ that receives chemical signals, which is involved in species-specific behaviors, including social and sexual behaviors. Muskrat (Ondatra zibethicus) has a sensitive VNO system that detects specific chemicals such as pheromones and hormones and induces seasonal breeding behaviors. The purpose of this study is to investigate the distributions and expression patterns of vomeronasal receptor type-1 (V1R), vomeronasal receptor type-2 (V2R), estrogen receptors α and β (ERα and ERβ) in the female muskrats’ VNO during the different periods. V1R, V2R, ERα and ERβ were found in sensory epithelial cells, non-sensory epithelial cells and lamina propria cells of the female muskrats’ VNO. V2R and ERα mRNA levels in the VNO of the breeding period declined sharply, in comparison to those of the non-breeding period, while V1R and ERβ mRNA levels were detected reversely. Additionally, a transcriptomic study in the VNO identified that differentially expressed genes might be related to estrogen signals and metabolic pathways. These findings suggested that the seasonal structural and functional changes of VNO in the female muskrats within different reproductive statuses, and estrogen regulated its function through binding to ERα and ERβ in the female muskrats’ VNO.