Prior to the introduction of the samples, we optimised and calibrated the GC–MS instrument, ensuring that it functioned within the established parameters (Supplementary Figure S1A). Subsequently, three parallel injections of the quality control samples were performed, revealing excellent overlap in retention times and peak areas, indicative of instrument stability (Supplementary Figure S1B). Furthermore, the analysis of blank samples showed no appreciable peaks, confirming the effective control of the material residue and the absence of cross-contamination between samples (Supplementary Figure S1B). A total of 99 volatile compounds of different groups of musk were successfully identified via GC–MS (Supplementary Tables S1-1 and S1-2). These compounds were divided into nine compound classifications, with the top three being 26 alcohols, 14 esters, and 14 ketones (Supplementary Figure S1C). According to the different proportions of the metabolite peak area, we found that organic acids accounted for the highest proportion of the total metabolites in white musk (65.28%), followed by other musks, and the lowest proportion in red-brown musk (15.18%) (Figure 2A). In contrast, the ketone content was the lowest in white musk (12.29%) and higher in other musks, with the highest observed for red-brown musk (36.60%) (Figure 2A). After analysing the musks as paste, ointment, powder, and strips according to their physical forms, we found that the proportion of organic acid in paste musk was the highest (65.09%) and showed a downward trend, reaching the lowest value in strips (15.07%) (Figure 2B). However, the proportion of ketones in paste musk was the lowest (14.64%), which showed an increasing trend and reached the highest value in strip musk (35.19%) (Figure 2B). Further analysis revealed that the proportion of organic acids in white musk was significantly greater than that in the other colours of musk, with the exceptions of yellow and light brown (Figure 2C). Additionally, the ketone content in white musk was notably lower than that in red-brown, dark brown, yellow-brown, brown, and black musk (Figure 2D). The organic acid content in paste musk was significantly higher than that in ointment, powder, and strip musk, with a gradual downward trend (Figure 2E). In contrast, its ketone content was markedly lower than in these forms, exhibiting a gradual upward trend (Figure 2F). The correlation heatmaps revealed that yellow musk, yellow-brown musk, red-brown musk, light brown musk, black musk, dark brown musk, and brown musk were highly correlated (r > 0.82), indicating that their compositions and contents are similar (Figure 2G). However, white musk had a low correlation with other-coloured musks (r < 0.69) and a large difference in composition (Figure 2G). When a correlation analysis was conducted on the basis of morphological classification, it was found that strip musk, ointment musk, and powder musk were highly correlated (r > 0.95), and their compositions and contents were similar, whereas paste musk and other forms of musk had large differences in composition and content (r < 0.58) (Figure 2H). Notably, the percentage of white musk in paste musk was significantly greater than that in the other colours (62.5%, 15/24) (Supplementary Figure S1D). These results indicate that the change in musk colour from light to dark may be accompanied by a decrease in organic acid content and an increase in ketones.