Using ‘Qinguan’、‘Fuji’、‘Golden delicious’ as apple materials to analysis the changes of phenolic content and relevant enzyme activities of pulp by inoculation with Botrytis cinerea Pers. The results provide a physiological theoretical basis for apple gray mold resistance. The results indicated that: (1) the size of disease incidence and lesion diameter in three apple varieties after the inoculation were ‘Qinguan’ < ‘Fuji’ < ‘Golden delicious’ (P<0.05), so all varieties of grey mold disease resistance were ‘Qinguan’> ‘Fuji’ > ‘Golden delicious’. (2) The phenylalanine ammonialyase (PAL), peroxidase (POD), poly phenol oxidase (PPO) activites in the pulp of resistant variety were higher than that in susceptible variety, and the contents of flavonoids and lignin were also higher significantly (P<0.05). Besides, the content of total phenolic compounds were ‘Qinguan’ < ‘Golden delicious’ < ‘Fuji’. In conclusion, resistant variety improved secondary metabolism by regulating phenolic metabolism to improve disease resistance in grey mold. The increasing content of flavonoids and lignin strengthened grey mold disease resistance of apple, but the total phenols content has little relation with the disease resistance.