The present study evaluated the antibacterial efficacy of Maclura tricuspidata root (MTroot) extracts against the cariogenic bacterium Streptococcus mutans. The chloroform (CHCl3) fraction obtained from organic solvent partitioning of the MTroot ethanol extract was subfractionated using open-column chromatography on silica gel. Among the subfractions obtained, subfraction 3 (Fra-3) obtained in 1:1 (v/v) n-hexan:ethyl acetate solvent system exhibited the most potent antibacterial activity. Accordingly, the chemical composition was analyzed using ultraperformance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry in positive electrospray ionization mode. In addition, the antibacterial activity of Fra-3 against S. mutans was assessed at each stage of extraction. While the minimum inhibitory concentrations (MICs) of the CHCl3, EtOAc, n-butanol, and aqueous fractions against S. mutans were above 15, 120, 120, and 120 μg/mL, respectively, the MICs of the subfractions obtained from silica gel open-column chromatography using different n-hexane:ethyl acetate ratios (3:1, 1:1, and 1:3) were 3.0, 1.5, and 25.0 μg/mL, respectively. Fra-3 was tentatively found to contain 38 major compounds, including kuwanon C, kuwanon E, cudratricusxanthone L, morusin C, cycloartocarpesin, kuwanon A, mulberrofuranol, and moracin U, which accounted for 66.7% of the total ion response. Collectively, these findings suggest that kuwanon C, kuwanon E, and cudratricusxanthone L present in MTroots may serve as novel therapeutic targets to prevent dental caries caused by S. mutans.