The root of Polygonum multiflorum Thunb. (Heshouwu in Chinese) is one of the most popular herbs used in traditional Chinese medicine (TCM). However, after steam processing (Zhi-heshouwu in Chinese), the root is known to have different properties and medicinal values compared with Heshouwu. Eleven volatile Maillard reaction products were identified in the extract of Zhi-heshouwu, but not in that of Heshouwu. The new products were four furanones, two furans, two nitrogen compounds, one pyran, one alcohol and one sulfur compound. The antioxidant activities were compared between the extracts from Zhi-heshouwu and Heshouwu. The results showed that the extract from Zhi-heshouwu presented a higher 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging activity than the extract from Heshouwu, with IC50 values of 0.43 mg/mL and 2.9 mg/mL, respectively (p < 0.05). The hydroxyl radical scavenging activities of the two were similar (IC50 0.98 mg/mL and 1.45 mg/mL, respectively; p > 0.05). 5-Hydroxymethyl-furfural, a main compound in the extract of Zhi-heshouwu, showed IC50 values for scavenging DPPH radicals and hydroxyl radicals of 1.6 mg/mL and 0.24 mg/mL, respectively. The antioxidant activities of the extract from Zhi-heshouwu could partly explain the different therapeutic effects of Heshouwu and Zhi-heshouwu in TCM.