Wood color is a crucial factor influencing the overall quality of wood products. In this study, we investigated color differences between sapwood (SW) and heartwood (HW) in 4 Chinese fir clones of the same age, using the CIE L*a*b* system. Our results revealed distinct color variations between SW and HW within the same clone, with notable discrepancies observed among different clones. Interestingly, these variation in wood color correlated with wood density, consistent with previous research. Metabolite analysis using an untargeted metabolomics approach was conducted, employing ultra-performance liquid chromatography in conjunction with a quadrupole time-of-flight tandem mass spectrometer (UPLC/Q-TOF–MS/MS), identifying a total of 938 metabolites spanning 12 superclasses. Principal Component Analysis (PCA) and Hierarchical Cluster Analysis (HCA) revealed distinct metabolic differences between SW and HW in various Chinese fir clones, with significant variations in abundance patterns and species-specific differences observed in the HW group. Further analysis, through Orthogonal Partial Least Squares-Discriminant Analysis (OPLS-DA), pinpointed specific metabolites responsible for these distinctions. Among these metabolites, flavonoids, recognized for their role in color formation, stood out prominently. Metabolomic pathway enrichment analysis (MPEA) indicated the involvement of these differential metabolites in various pathways, including flavonoid biosynthesis. The study underscores the intricate relationship between metabolites and wood color variation in Chinese fir clones, accentuating potential applications in enhancing wood quality and decay to resistance.