A combination of methods (e.g. scan sampling, focal sampling, all-occurrence recording methods), was used to collect behavioral information on 45 forest musk deer at Maerkang Musk Deer Breed Center, Sichuan Province of China. More specifically, we measured the frequency of non-resting behaviors and the intensity of affinitive behaviors. The aim of the study was to assess how gender, group size and social affinity influenced captive musk deer’s activity. The results show significant effect group size and social affinity on activity (P < 0.05), but not gender (P > 0.05) as the activity level of males did not differ from that of females. Indeed, we found that individuals were more active when in groups of smaller size (0.40 ± 0.022, n = 4) as compared to large size groups (0.25 ± 0.021, n = 32); and that activity level increased with social affinity (r = 0.390, P = 0.01), with highly active individuals holding highly social individuals. This study suggests that the individual difference in activity among groups of different in sizes may be used to carry out recommendations on change in herds’ structure and composition aimed at facilitating social cohesion and achieving more efficient management procedure in musk deer herds.