Flavonoids represent a large group of polyphenols that have been recognized to exert a wide range of biological effects, such as anticancer, inflammation inhibition, anti-aging, and neuroprotective activities. In the forest industry, tree twigs have been treated as residues; however, tree twigs could be a rich source of high-value added compounds, which have been relatively unexplored. In this study, an investigation into the chemical constituent of extractives from S. japonica twigs resulted in the isolation of a new (Z)-caffeoyl flavonol glycoside that was elucidated as myricetin 3-O-(4′′-(Z)-caffeoyl)-α-rhamnopyranoside (IV). The structure of the new compound was established mostly on the basis of extensive spectroscopic techniques and other physiochemical evidences. Among the three known flavonoids extracted in this work, including isoquercitrin (I), isorhamnetin 3′-O-β-D-glucopyranoside (II), and myricitrin (III), II and III have never been previously reported in the Sophora genus.