•UV-C treatment significantly increased the content of total phenolics, flavonoids, and anthocyanins.•UV-C irradiation enhanced the enzymes activities of PAL, C4H, and 4CL.•UV-C treatment induced the expression of the key phenylpropanoid pathway genes.•Bioactive compounds are co-related with phenylpropanoid pathway biosynthesis. Ultraviolet (UV) influences postharvest changes in secondary metabolites of fruit. In this study, sweet cherries were treated with UV-C irradiation (1.05, 2.10, and 4.20 kJ/m2) for different treatment periods, they were stored at room temperature (25.0 ± 2.0 ℃) for 6 days. The results showed that the total phenolics, flavonoids, and anthocyanins increased in response to UV-C during storage. UPLC-ESI-MS analysis indicated that the individual flavonoids and anthocyanins contents increased, including cyanidin 3-O-galactoside, cyanidin O-syringic acid, cyanidin 3-O-glucoside, pelargonidin 3-O-glucoside, tricin 5-O-hexoside, luteolin C-hexoside, Di-O-methylquercetin, and naringenin-7-O-glucoside. Furthermore, UV-C (2.10 kJ/m2) treatment upregulated the enzymes activity and genes expression of phenylpropanoid pathway. Highly significant correlations were found among flavonoids, anthocyanins, phenylalanine ammonia lyase (PAL) and genes expression of ANS, DFR, UFGT (r > 0.6, p < 0.01) and cinnamate 4-hydroxylase (C4H) and PAL, C4H, 4CL, CHI, ANS, DFR expressions (r> 0.6, p < 0.01). These results contribute to illustrating the molecular mechanism of flavonoids and anthocyanins biosynthesis under the UV-C irradiation in sweet cherries and promote the development of postharvest in agriculture.