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Heartwood has a high economic value because of its natural durability, beautiful color, special aroma, and richness in active ingredients used in traditional Chinese medicine. However, the mechanism of heartwood formation remains unclear. Dalbergia odorifera was selected as the object of research to analyze this variation in the chemical composition of sapwood, transition zone, and heartwood as well as to elucidate the relationship between this variation and the formation of heartwood. The variation of secondary metabolites was analyzed using gas chromatography-mass spectrometry and ultra-high performance liquid chromatography–mass spectrometry, the variation of lignin was analyzed using Fourier transform infrared spectroscopy and ultraviolet visible spectrophotometry, and the variation law of mineral elements was analyzed using atomic absorption spectrophotometry. The results demonstrated that contents of characteristic secondary metabolites in Dalbergia odorifera were mainly distributed in heartwood (84.3–96.8%), increased from the outer to inner layers of the xylem, and sudden changes occurred in the transition zone (the fourth growth ring). The Dalbergia odorifera lignin can be identified as typical "syringyl–guaiacyl (S–G)" lignin, and the color darkened from the outside to the inside. The results demonstrated that there were more benzene rings and conjugated C=O structures in the heartwood. Additionally, the variation of minerals in the xylem was related to elemental types; the average concentrations of Mg, Ca, Fe and Sr were higher in the heartwood than in the sapwood, whereas the concentrations of K and Zn were higher in the sapwood than in the heartwood owing to the reabsorption of elements. The concentrations of Na and Cu were similar in the heartwood and sapwood. The composition and structural characteristics of secondary metabolites, lignin, and mineral elements in the three typical xylem regions (sapwood, transition zone and heartwood) of Dalbergia odorifera changed. The most abrupt change occurred in the narrow xylem transition zone, which is the key location involved in heartwood formation in Dalbergia odorifera. [ABSTRACT FROM AUTHOR]