Abstract Flavonoids make a very important contribution to the organoleptic qualities of grapes and wines. In this work these were analyzed in Cabernet Sauvignon grown in Changli, Hebei Province in east China and Gaotai, Gansu Province in west China. These regions have distinctly different climates contributing to their different ‘terroir’. RNA sequencing was performed to trace transcriptome changes in Cabernet Sauvignon berries at pea size, veraison and ripening, corresponding to E-L 31, 35 and 38. The accumulation of flavonols, flavan-3-ols and anthocyanins together with the expression of relevant genes were analyzed and compared between the two regions. The biosynthesis patterns were similar between two regions, but more flavonols, anthocyanins, and tri-hydroxylated flavonoids accumulated in grapes from Gaotai before berry harvest, possibly due to the higher transcript levels of the genes that encode biosynthetic enzymes and their potential candidate transcription factors. The lower levels of flavan-3-ols, mainly (−)-epigallocatechin, in the pre-veraison grapes from Changli, might be due to limited flow of carbon to the F3′5′H branch pathway, as the ratio of F3′5′H to F3′H was lower in these berries from Changli. It is suggested that the combination of climatic factors profoundly affect the flavonoid pathway in grapes from China, providing regionally specific metabolism patterns.