With the aim of explaining how russet was prevented in the mutant, we analyzed the components of the secondary metabolites in the peels and found that ‘Feng Shuai’ apple contained more total flavonoids and chlorogenic acid (CA) than the wild type ‘Golden Delicious’ at the early stage of fruit development. So the hypothesis was made that the higher level of CA might be associated with inhibition of fruit russet formation. This hypothesis was tested through field application experiments, and its biochemical and molecular bases were further analyzed in this study.