Captivity is one of the main methods to protect wild Forest Musk Deer (Moschus berezovskii) in China. However, parasitic disease is the main factor limiting the reproduction of captive individuals in the process of population rejuvenation. To investigate the response of parasite community in the digestive tract to different perturbations, we performed a perturbation experiment in captive Forest Musk Deer, by using compound drug albendazole ivermectin powder and single drug avermectin powder to suppress macroparasites, and monitored the consequences of dynamic changes in its community and other parasite species. We randomly selected 60 adult male Forest Musk Deers and divided them into different treatment groups: albendazole ivermectin group (20 ind), avermectin group (20 ind), and control group (20 ind), the control group without any treatment. We collected fresh fecal samples after anthelmintic disturbance for eight weeks for the experiment of egg floatation and count of eggs and oocysts based on Wisconsin’s egg counting method. Then we did the Kruskal-Wallis test, Wilcoxon test, Mann Whitney test, and Two-way ANOVA test of the data. The results showed that the parasite infection of Forest Musk Deer was mixed in both control group and albendazole ivermectin group after anthelmintic treatment, with coccidia being the dominant parasite taxa. The number of coccidia was higher than that of nematode or cestode (P < 0.05) (Fig. 1). In the avermectin group, only coccidia was found (Fig. 1). The prevalence and average infection intensity of coccidia in treatment group were higher than those in the control group after interference, while treated Forest Musk Deers had a lower (27.15%) nematode infection rate compared with control individuals (42.15%) (Fig. 1, Fig. 2). The reinfection of nematode and cestode in albendazole ivermectin group was quicker than that in avermectin group after interference (Fig. 4, Fig. 5). Therefore, this study has proved that parasitic infection of digestive tract is common in Forest Musk Deer, and that competitive interactions between multiple parasite infections exist in the digestive tract. The analysis of community dynamics indicated that parasite communities in the digestive tract have diverse responses to different disturbance strategies, and that the compound medicine can cause greater perturbation to the coccidia and the recovery ability of parasite community is in proportion to perturbation degree. These results have provided a rare and clear experimental demonstration of interactions between helminths and co-infecting parasites in wild vertebrates. We suggested that the Forest Musk Deer breeding center should strengthen scientific and planned deworming, and continuously monitor parasite infection.