The phytochemical investigation of the roots of the traditional Chinese medicinal plant Sophora flavescens led to the isolation of two novel prenylflavonoids with an unusual cyclohexyl substituent instead of the common aromatic ring B, named 4′,4′-dimethoxy-sophvein (17) and sophvein-4′-one (18), and 34 known compounds (1–16, 19–36). The structures of these chemical compounds were determined by spectroscopic techniques, including 1D-, 2D-NMR, and HRESIMS data. Furthermore, evaluations of nitric oxide (NO) production inhibitory activity against lipopolysaccharide (LPS)-treated RAW264.7 cells indicated that some compounds exhibited obvious inhibition effects, with IC₅₀ ranged from 4.6 ± 1.1 to 14.4 ± 0.4 μM. Moreover, additional research demonstrated that some compounds inhibited the growth of HepG2 cells, with an IC₅₀ ranging from 0.46 ± 0.1 to 48.6 ± 0.8 μM. These results suggest that flavonoid derivatives from the roots of S. flavescens can be used as a latent source of antiproliferative or anti-inflammatory agents.