The fruit of Schisandra chinensis, namely "Wuweizi" in China, is a well-known herbal medicine and health food. In this paper, an accurate and reliable high performance liquid chromatography coupled with diode array detection and mass spectrometry was developed for quality evaluation of Wuweizi. Nine lignans, including schisandrol A, schisandrol B, angeloylgomisin H, gomisin G, schisantherin A, schisanhenol, schisandrin A, schisandrin B, and schisandrin C were determined simultaneously in forty-three batches of Wuweizi samples collected from different localities. Thirty-six common peaks were unequivocally identified or tentatively assigned by comparing their mass spectrometric data with reference compounds, self-established compound library and published literatures. And the thirty-six common peaks were selected as characteristic peaks to assess the similarity of chromatographic fingerprinting of these Wuweizi samples. Moreover, hierarchical clustering analysis and principal components analysis were successfully applied to demonstrate the variability of these Wuweizi samples. The results indicated the content of nine investigated lignans varied greatly among the samples, and samples collected from different localities could be discriminated. Furthermore, schisandrol A, schisandrol B, schisandrin B, and schisandrin C were found to chemical marker for evaluating the quality of Wuweizi.