Male forest musk deer undergo a seasonal musk secretion period accompanied by pronounced physiological and behavioral changes. However, whether endocrine and metabolic remodeling, feeding-related changes, and gut microbiome variation occur together within individuals during this period remains unclear. We conducted a paired within-individual study of captive adult males sampled before and during musk secretion over an approximately three-week interval. Serum hormone profiles, untargeted serum metabolomics, fecal 16S rRNA gene sequencing, and husbandry records of feed intake, activity, and resting time were integrated to characterize this seasonal transition. Compared with the pre-secretion stage, serum testosterone, estradiol, and progesterone were higher during secretion, whereas thyroxine and cortisol did not differ significantly. Untargeted LC–MS profiles showed higher androgen conjugates, 2-methoxy-17β-estradiol, and cortisol/cortisone-related signals during secretion, together with lower pregnanediol and thyroxine-related signals. Recorded feed intake and activity decreased markedly, whereas resting time increased. Fecal microbiome analyses showed lower Shannon diversity during secretion; distance-based community structure also differed between stages, alongside greater community dispersion during secretion. Eleven bacterial genera or genus-level assignments met the differential-abundance criterion, although these findings showed limited robustness in sensitivity diagnostics. Exploratory within-individual analyses further showed that changes in feed intake were negatively associated with changes in an unclassified Micrococcaceae genus (Spearman ρ = −0.921, q = 0.014) after multiple-testing correction. Musk secretion in male forest musk deer coincided with a broader seasonal physiological transition involving endocrine and metabolomic remodeling, reduced feed intake and activity, increased resting time, and restructuring of the gut microbiome. Because these changes occurred concurrently in this observational study, their causal ordering cannot be resolved. These findings provide a paired physiological and microbiome baseline for forest musk deer and a foundation for future longitudinal and non-invasive studies of physiologically demanding seasonal periods in captive and wild mammals.