Flash evaporation-gas chromatography/mass spectrometry (FE-GC/MS) with 0.3 mg sample powder in a vertical microfurnace pyrolyzer at 300 °C was applied to analyze Schisandra fruits without any tedious pretreatment. In total, 80 compounds, 74 compounds of which were identified, were observed, including low-molecular-weight compounds, essential oils (especially terpenoids), fatty acids and esters, and lignans, with the relative standard deviations (RSDs) of the relative percent of peak areas less than 7.79 % (n = 5). 32 compounds of terpenoids and lignans were selected as fingerprint components, since they are the main bioactive constituents in Schisandra fruits. The standard characteristic fingerprints of S. chinensis fruits and S. sphenantherae fruits were established, based on the 32 fingerprint components of 11 genuine S. chinensis fruit samples and 9 genuine S. sphenantherae fruit samples. The discrimination of samples from different growing places was achieved by principle component analysis and hierarchical cluster analysis. Furthermore, a similarity evaluation method was developed to evaluate the quality of each Schisandra fruit sample on the basis of the 32 fingerprint components. The results proved that the FE-GC fingerprint combined with a chemometric approach is a simple, rapid, and effective method for the origin discrimination and quality control of Schisandra fruits.