The root of Millettia speciosa Champ. (MSCP) is used in folk medicine and is popular as a soup ingredient. The root is composed of the rhizome and radix, but only the radix has been used as a food. Thus, it is very important to compare the chemical components and antioxidant activities between the rhizome and radix. The extracts were analyzed by UHPLC-Q-Exactive Orbitrap-MS and multivariate analysis, and the antioxidant activities were evaluated by 2,20-azinobis (3-ethylbenzothiazo-line-6-sulfonic acid) diammonium salt (ABTS) and 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging assays. Ninety-one compounds were detected simultaneously and temporarily identified. Ten compounds were identified as chemical markers to distinguish the rhizome from the radix. The antioxidant activities of the radix were higher than the rhizome. Correlation analysis showed that uvaol-3-caffeate, 3-O-caffeoyloleanolic acid, and khrinone E were the main active markers for antioxidant activity, which allowed for the rapid differentiation of rhizomes and the radix. Therefore, it could be helpful for future exploration of its material base and bioactive mechanism. In addition, it would be considered to be used as a new method for the quality control of M. speciosa.