ABSTRACT Lily is an economically important ornamental and edible plant, and its commercial value is highly dependent on flower colour. This study investigated the mechanism of colour variation using an orange‐flowered cultivar ‘Orange Matrix’ and its natural golden‐yellow petal mutant. The results demonstrated no significant difference in total carotenoid content between the petals of the two lily plant varieties. The distinct coloration was determined by the composition and proportion of specific carotenoid metabolites. The predominant pigments in orange petals were zeaxanthin and capsanthin, whereas yellow petals demonstrated reduced capsanthin, thus leading to lutein, antheraxanthin, and zeaxanthin dominance, which shifted the colour to golden yellow. Functional analysis revealed that LmCCS induces the synthesis of capsanthin, concurrently regulating the metabolic flux from lycopene into various branches of the carotenoid biosynthesis pathway. In GM, the downregulation of LmCCS expression directly reduces the content of capsanthin in petals and significantly increases the β,ε‐/β,β‐carotenoid ratio, thereby promoting the accumulation of lutein and the formation of yellow petals. Suppression of LmCCS via virus‐induced gene silencing diminished the orange coloration and enhanced the yellow colour in lily petals. Furthermore, the expression level of LmAPRR2 was consistently negatively correlated with LmCCS . Dual‐luciferase reporter assays and yeast one‐hybrid experiments demonstrated that the LmAPRR2 protein directly binds to the LmCCS promoter to repress its transcription. Our findings provide novel insights into the regulatory network of carotenoid metabolism and flower colour formation in lilies.