Anthocyanins and hydroxycinnamic acid derivatives in the crude extracts of peel, flesh, and whole roots of 10 Chinese purple-fleshed sweetpotato genotypes were simultaneously characterized by liquid chromatography-photodiode array detector-atmospheric pressure chemical ionization-mass spectrometry (LC-PDA-APCI-MS), as well as their antioxidant activities were systematically investigated and compared. Major anthocyanins were identified as peonidin or cyanidin 3-sophoroside-5-glucoside and their acylated derivatives, e.g., peonidin 3-sophoroside-5-glucoside, peonidin 3-(6''-p-feruloylsophoroside)-5-glucoside, and cyanidin 3-(6''-p-feruloylsophoroside)-5-glucoside, and main hydroxycinnamic acid derivatives were identified as mono- and dicaffeoylquinic acids (e.g., 5-O-caffeoylquinic acid and 3,5-di-O-caffeoylquinic acid) and caffeoyl-hexoside. These main phenolic compounds identified were important contributors to the total antioxidant capacity of the tested sweetpotato samples. Additionally, great variations in contents of both total and individual phenolic compounds as well as antioxidant activities between different genotypes and among various parts of the roots were observed. This study may provide value information for breeding new lines of Chinese purple-fleshed sweetpotato and also for quality control of bioactive components during production and processing.