Honey is a nutrient-rich natural functional food, with its color being considered as a key indicator of quality and consumer acceptance. Although various secondary metabolites are closely related to the color of honey, the specific substances and their exact effects on honey color remain unclear. In this study, the chemical composition, such as organic acids, polyphenols and vitamins, in different colored honey (Acacia, buckwheat, linden, vitex, lychee and jujube honey) were quantitatively analyzed using liquid chromatography-high resolution mass spectrometry (LCHRMS). The correlations between the chemical composition and the honey color were established by the mantel test. The results showed that quinic acid, ascorbic acid, and other composition were identified as significantly related with honey color. The validation experiments indicated that adding these significantly related substances to honey samples could multiplicatively deepen the honey color, and the value of the deepening color was positively correlated with that of the initial color. The study developed a practical and systematic LCHRMS method for analyzing chemical composition in honey. The results provided valuable scientific insights into the relationship between chemical composition and honey color. Additionally, it introduced a novel and feasible approach for investigating the effects of substances on the color of complex mixture systems.