Abstract: Male muskrats（Ondatra zibethica） have the special glands called scented glands. There are obvious periodic changes in the morphology and function of scented gland. In the secreted period, the scented gland gradually expands and secretes a large amount of musk. Muskrat musk plays an important role in information communication among individuals. In the non-secreted period, the scented glands atrophy and degenerate, and no longer secrete musk. At present, there were few studies on the regulation mechanism of periodic changes in the scented gland of muskrat. In this study, transcriptome technique was used to analyze the changes of regulatory pathways in the cells of scented gland of muskrat during and non-secreted period. The results showed that complement and coagulation cascade, phosphatidylinositol signaling system, janus kinase-signal transducer and activator of transcription（JAK-STAT） signaling pathway and mitogen-activated protein kinase（MAPK） signaling pathway were annotated. At the same time, compared with the secreted period, the expression of genes in the above pathways was significantly increased in the tissues of the non-secreted period, which was consistent with the process of periodic degeneration of scented glands. Therefore, the complement and coagulation cascade, phosphatidylinositol signaling system, JAK-STAT signaling pathway and MAPK signaling pathway might play a regulatory role in the periodic degeneration of scented gland. This study preliminarily explored the pathway regulation process of periodic changes of scented gland in muskrat.