We investigated the genetic diversity of the population of captive forest musk deer (Moschus berezovskii) in Barkam Musk Deer Breeding Centre using twelve microsatellite markers, and then analyzed the change in genetic structure of successive generation groups from the population. The data provide a new understanding for the evaluation and usage of the breeding management system. Microsatellite marker analysis detected 141 alleles with an average of 11.75 alleles for each marker. The average expected heterozygosity (HE) was 0.731. Performing an F-statistical analysis on the data showed that the genetic diversity of population decreased, and the inbreeding coefficient significant increased with the increase of generation, and FIS of the 1st generation is significantly lower than that of the second to fifth generation (p < 0.01). The result suggested that the captive population was facing the pressure of inbreeding (FIS = 0.115) and the subsequent loss of genetic diversity. Therefore, it is necessary to improve the breeding management system of the captive population by preventing close relatives from mating or inducing new individuals from the exotic population.