Phytochemical study on the aerial parts of Yua thomsonii resulted in the isolation of 11 secondary metabolites, including a new caffeoyl quinic acid derivative, 3-O-trans-caffeoyl-4-Oacetylquinic acid methyl ester (1), a new dihydrobenzofuran neolignan, 3,5-dimethoxy-4-(1,3dihydroxy-2-propyloxyl)-4,7-epoxy-8,5-neolignan-4,9,9-triol (3), and nine known compounds, methyl 4-O-coumaroylquinate (2), (7S * ,8S * )-3-methoxy-3ʹ,7-epoxy-8,4ʹ-oxyneolignan-4,9,9ʹ-triol (4), kompasinol A (5), lyoniresinol (6), schizandriside ( 7), (−)-isolariciresinol 3a-O-β-Dxylopyranoside (8), lyoniside (9), vitexin (10), and luteolin 4-O--glucopyranoside (11). Their structures were elucidated using comprehensive spectroscopic methods, including 1D and 2D NMR and HRESI mass spectra. The absolute configurations of 1 and 3 were deduced by electronic circular dichroism (ECD) spectroscopy. Compounds 1, 3, 5, and 6 exhibited nitric oxide (NO) inhibitory effects, with IC50 values ranging from 12.18−29.45 M. However, compounds 1, 3, 6, and 8 were non-cytotoxic toward HepG2 and MCF-7 carcinoma cells.