•We find that the endogenous chlorogenic acid levels were closely related with fruit russet index.•When exogenous CA was treated, fruit russeting of Golden Delicious apple was blocked.•CA treatments affect enzyme activities and regulate gene expression in phenylpropanoid route.•CA treatment regulates secondary metabolism of apple peels which is related with russet formation. Analysis of the secondary metabolites in apple peels showed that the levels of total flavonoids and chlorogenic acid (CA) during 15–60 days after full bloom (DAFB) were significantly higher in cultivar ‘Feng Shuai’, a spontaneous non-russeting mutant of ‘Golden Delicious’ apple, than in its maternal plant, which indicated higher level of endogenous CA may be associated with the inhibition of russet formation. Application of 0.5mmolL−1 exogenous CA solution to ‘Golden Delicious’ fruits at 30 DAFB effectively inhibited fruit russet formation. It also increased the levels of CA and total flavonoids in fruit peels at the 7th day after treatment, but depressed the lignin content. Furthermore, CA treatment induced the activity of phenylalnine ammonialyase (PAL) and cinnamate-4-hydrolase (C4H), but depressed activity of polyphenol oxidase (PPO) and peroxidase (POD). These effects were further supported by RT-PCR, where the expressions of PAL, C4H, 4CL, CHS, and CHI were up-regulated while those of CAD, POD and PPO were down-regulated by CA treatment. Interestingly, the up-regulated genes are involved in the biosynthesis of chlorogenic acid and flavonoids while the down-regulated ones are involved in lignin biosynthesis. Therefore, it can be deduced that the inhibition of russet formation in ‘Golden Delicious’ apple by CA is associated with the inhibition of lignin biosynthesis, not the enhancement of total flavonoids biosynthesis.