•Chlorophyll and carotenoids content changed with seasons in U. pumila leaves.•Flavonoids gradually accumulated with seasonal changes in U. pumila leaves.•UpCrtR-b could significantly increase carotenoid accumulation. Ulmus pumila ‘Zhonghua Jinye’ is an important landscape tree species because of its golden leaves. Leaf coloration is the main factor that determines the ornamental and economic value of U. pumila. Gene expression and metabolite accumulation patterns were studied by transcriptome and metabolome to explore the physiological and molecular mechanisms of leaf color changes in U. pumila. The results showed that the leaf color change of U. pumila was regulated by the metabolism of chlorophyll, flavonoids, and carotenoids. The content of total chlorophyll and chlorophyll a decreased gradually with seasonal changes, which was mainly caused by the obstruction of chlorophyll synthesis and the activation of the chlorophyll degradation pathway. Among them, the expression level of chlorophyll synthesis-related genes (GluTR, UROD, PPO, and POR) were down-regulated, while certain genes (CHLG, CAO, HCAR, PPH, and PAO) in the chlorophyll degradation pathway were significantly up-regulated. In addition, flavonoids gradually accumulated with seasonal changes. Among them, twenty-six key genes (PAL, 4CL, CHS, F3H, FLS, 3GT, DFR, and ANS) in flavonoid biosynthesis were involved in regulation of flavonol and anthocyanin biosynthesis. Furthermore, carotenoids (lutein, zeaxanthin, and β-carotene) were also mainly accumulated in July and August. Finally, the candidate gene, UpCrtR-b, in carotenoid biosynthesis was identified in the present study and was found to be expressed in plastids by functional verification. In tobacco, overexpression of UpCrtR-b could increase carotenoid accumulation and make tobacco leaves yellowish. This study revealed the molecular mechanism of leaf color regulation in U. pumila, and provided a theoretical basis for better utilization of this species as a landscape tree, which also provides the possibility for further enriching the variation mechanism and cultivating colored leaf plants. Display omitted