Wild Alpine musk deer (Moschus chrysogaster), which are native to the Qinghai-Tibet Plateau and surrounding areas, have been kept in captivity as an effective way to conserve musk deer ex situ and sustainably utilize musk resources. From 1 November to 31 December of 2019, the behaviors of 40 captive Alpine musk deer in Xinglongshan Musk Deer Farm (XMDF) in Gansu Province of western China were sampled by focal sampling and the all-occurrence recording method. Moreover, harvested musk was analyzed for muscone using gas chromatography (GC), and the adrenal cortisol metabolite levels of fecal samples were detected by radioimmunoassay (RIA). The effects of social housing modes (solitary deer per enclosure [SE] or group enclosures [GE]) on the behavior, hormones, and musk secretion of musk deer were investigated. The results showed that most captive male musk deer (75.0%) in the XMDF exhibited stereotypic behavior, with an average duration of stereotypic behaviors of 8.8% ( ± 0.5%) of the total observation time. The fecal cortisol metabolite level of musk deer with stereotypic behavior (48.1 ± 4.3 ng/g) was significantly higher than that of musk deer without stereotypic behavior (33.5 ± 6.6 ng/g). The proportion of stereotypic behavior was significantly lower in SE musk deer (50.0%) than in GE musk deer (83.3%), and the duration of stereotypic behavior (7.3% ± 0.3%) and fecal cortisol metabolite level (29.9 ± 3.1 ng/g) of the SE deer were significantly lower than those of GE (9.2% ± 0.6%; 49.4 ± 4.5 ng/g). There was no significant difference in musk yield and muscone content between SE musk deer (5.8 ± 1.4 g, 1.5% ± 0.3%) and GE musk deer (7.4 ± 0.8 g, 1.0% ± 0.1%). The results showed that the social housing mode is not significantly related to musk yield, muscone, or other performance indicators. It also showed that the stereotypic behavior and cortisol metabolites are significantly lower in SE musk deer. Therefore, we concluded that the animal welfare of captive musk deer can be improved through changes in social housing modes.