The dried roots of Polygonum multiflorum Thunb. (Heshouwu) and their processed products (Zhi-heshouwu) are widely used in traditional Chinese medicine, yet their therapeutic effects are different. Previous investigations focused mainly on the differences between Heshouwu and Zhi-heshouwu in the contents of several known compounds. In this study, a rapid resolution liquid chromatography-diode array detection/electrospray ionization tandem mass spectrometry (RRLC/DAD/ESI-MS(n)) method was developed for the comparative analysis of the components of Heshouwu and Zhi-heshouwu. A total of 23 compounds were identified or tentatively characterized. We found that 16 batches of Heshouwu and 15 batches of Zhi-heshouwu samples shared eight compounds, including gallic acid; 3,5,4'-tetrahydroxylstilbene-2,3-di-O-glucoside, CIS-2,3,5,4'-tetrahydroxylstilbene-2-O- β-D-glucoside, trans-2,3,5,4'-tetrahydroxylstilbene-2-O- β-D-glucoside, emodin-8-O- β-D-glucoside, physcion-8-O- β-D-glucoside, emodin, and physcion. Nevertheless, the relative amounts of gallic acid, emodin, and physcion were very high in Zhi-heshouwu samples compared to those in Heshouwu samples. Six compounds disappeared after processing and were unique for Heshouwu: catechin, flavanol gallate dimer, polygonimitin B, emodin-1-O-glucoside, emodin-8-O-(6'-O-malonyl)-glucoside, and physcion-8-O-(6'-O-malonyl)-glucoside. Three compounds were unique for Zhi-heshouwu: hydroxymaltol, 2,3-dihydro-3,5-dihydroxy-6-methyl-4(H)-pyran-4-one, and 5-hydroxymethyl furfural. These results suggest that the types and relative amounts of the chemical components of Heshouwu and Zhi-heshouwu are different.