Rosa rugosa, an ornamental plant with medicinal properties, and its red-colored hips are rich in bioactive compounds. However, limited research has been conducted on the accumulation of pigments in its hips and the molecular regulatory mechanism. A comprehensive analysis of carotenoid metabolites at three different stages (mature green (MG), breaker (B) and mature red (MR)) in R. rugosa hips was performed using UPLC-APCI-MS/MS. A total of 18 carotenoids, including eight carotenes and ten xanthophylls, were identified, and their different accumulation patterns were observed in distinct stages. The analysis of differentially expressed genes (DEGs) using gene ontology (GO) highlighted 28 terms. The KEGG pathway analysis revealed that enriched pathways in the biosynthesis of secondary metabolites in MG versus B. RrGGPPS1 was identified as the producer of geranylgeranyl diphosphate (GGPP) through a genetic complementation assay in Escherichia coli and in vitro enzymatic assay. Furthermore, transiently silencing the RrGGPPS1 gene in rose resulted in the reduction of carotenoids in petals. This study provides a foundation for future research on understanding the regulation and biosynthesis of carotenoid metabolism in R. rugosa hips.