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Among ornamental plants, the colour of the petals is an important feature. However, the reason for the colour differences of <i>Rhododendron liliiflorum</i> remains unclear. To reveal the differences in the colour of <i>R. liliiflorum</i>, high-efficiency liquid chromatographic collar (UPLC–MS/MS) technology was used to study the yellow and white parts of <i>R. liliiflorum</i>. A total of 1187 metabolites were identified in <i>R. liliiflorum</i> petals, including 339 flavonoid metabolites. Seventy-eight types of flavonoids in these metabolites were found in the yellow and white parts of <i>R. liliiflorum</i> petals, along with 11 other significantly enriched substances. Combining gene expression-related data with differential metabolite data demonstrated effects of enrichment in the flavanonols (fustin), flavonols (epiafzelechin and afzelechin), and flavanones (pinocembrin) of flavonoid biosynthesis; glyccitin, 6″-O-malonylgenistin, and 6-hydroxydaidzein of isoflavonoid biosynthesis; and anthocyanin biosynthesis of malvidin-3-O-galactoside (primulin), delphinidin-3-O-rutinoside, cyanidin-3-O-glucoside (kuromanin), and cyanidin-3-O-rutinoside (keracyanin), which are potentially the contributing factors responsible for the differences in petal colour in <i>R. liliiflorum</i>. This study establishes a connection between the differential metabolites underlying the color differences in the petals of <i>R. liliiflorum</i> and the gene expression in <i>R. liliiflorum</i>. This will provide a foundation for subsequent research on the regulation of flower color in <i>R. liliiflorum</i> and have profound implications for horticultural applications of <i>R. liliiflorum</i>.