In this experiment, the effect of melatonin on hair follicle cell apoptosis and related mechanisms in angora rabbits were studied. A total of 60 angora rabbits were randomly divided into 4 groups. In group 1, no melatonin was implanted as a control group. In the other three groups, melatonin was implanted 25 mg (low dose group), 40 mg (middle dose group) and 55 mg (high dose group), respectively. After 70 days of feeding, pathological observation and RNA transcriptome high-throughput sequencing and qPCR expression analysis were performed. The tissue slicing results showed that 55 mg melatonin treatment could effectively inhibit the apoptosis of hair follicle cells and maintain the normal morphology of cells. Twenty–five differentially expressed genes were obtained by sequencing the high dose group and the control group, including 14 up–regulated genes and 11 down–regulated genes. These genes were involved pathways such as HTLV–I infection, necroptosis, thyroid cancer, ferroptosis, type I diabetes mellitus and insulin signaling pathway. Necroptosis and ferroptosis were related to apoptosis of hair follicles in angora rabbits. Four apoptosis–related differentially expressed genes were selected for fluorescence quantitative verification. As a result, the expression of MSTRG.3561 gene was significantly up–regulated and the expression of SLC25A5 was down–regulated, but no significant difference was found.