Phenolic composition and antioxidant capacity of different fruit part including peel, pulp, juice, whole fruit and seed from five lemon cultivars (Feiminailao, Cuningmeng Limeng, Pangdelusaningmeng, Beijingningmeng) were investigated. Caffeic acid (9.31-741.4 lg/g FW) and chlorogenic acid (2.7-527.5 lg/g FW) were the dominant phenolic acid in fruit tested, Pangdelusaningmeng (PD) and Limeng peels with the highest contents, respectively. Hesperidin was the predominant flavanone (10.27-3315 lg/g FW), Cuningmeng (CN) peels with the highest level. PD peels had rich rutin, CN seeds had rich eriocitrin. Nobiletin was the main polymethoxylated flavonoids identified, PD with the highest level. CN peels contained rich tangeretin. Overall, peels and whole fruit had significantly higher level of phenolics than other fruit parts, and seeds were good source of flavonoids. PD and CN not only contained higher level of phenolic, but also presented higher antioxidant capacity than other cultivars tested, and are of great value for human nutrition.