Both wild population rebuilding and sustainable musk yields require a healthy and growing population of musk deer (Moschus berezovskii) in captivity. Challenges of maintaining such a population come from irregular and frequent disease outbreaks. Meanwhile, disease monitoring and prediction require musk deer's baseline levels of physiology, which has been extremely lacking due to the high level of endangerment and limited availability of samples. In order to provide baseline physiology for disease monitoring, we non-invasively collected fecal samples from two captive populations of musk deer in Huoshaodian, Shaanxi, and Miyaluo, Sichuan in China, between July and August of 2014, and applied enzyme-linked immunosorbent assay (ELISA) method to estimate the concentrations and dynamics of fecal triiodothyronine (T3) among females. We found there was no significant difference of T3 concentrations between two populations during the study period. T3 concentrations first showed a universally growing trend with age from the age of 3 to 5, and then decreased after the age of 5 years. It might suggest that female musk deers reach physiological maturity at age 5. By clustering fecal T3 levels, we found significant differences among individuals at each age group, all of which could be assigned into low, medium and high metabolicgroups. We suggest the fecal T3 level, an index reflecting individual's metabolic characteristics of individuals, could be used to unveil physiological status of female musk deers, which has great potential in captive population establishment and management, as well as health condition evaluations.