The quality control of Polygala tenuifolia Wild. is a major challenge in its clinical application. In this paper, a new strategy for the quality evaluation of P. tenuifolia extracts was verified through reverse-phase ultra-performance liquid chromatography (UPLC). The quantitative analysis of multi-components by a single marker (QAMS) was conducted with 3,6′-disinapoyl sucrose as an internal reference substance. Eight components (i.e., sibiricose A5, sibiricose A6, glomeratose A, tenuifoliside A, tenuifoliside B, tenuifoliside C, sibiricaxanthone B, and polygalaxanthone III) were determined based on the relative correction factors. The concentrations of these components were also determined by applying a conventional external standard method. The cosine value confirmed the consistency of the two methods (cosine ratio value >0.999920). Hierarchical cluster analysis, radar plots, and discriminant analysis were performed to classify 23 batches of P. tenuifolia extracts from Shanxi, Hebei, and Shaanxi in China. Results revealed that QAMS combined with radar plots and multivariate data analysis could accurately measure and clearly distinguish the different quality samples of P. tenuifolia. Hence, QAMS is a feasible and promising method for the quality control of P. tenuifolia.