Display omitted •E-eye, E-nose and HS-GC-MS jointly solved the authenticity problems of ZSS.•SVM, KNN and ANN algorithms successfully distinguish ZSS from adulterants.•The rapid discriminant formulas to distinguish ZSS and adulterants based on E-eye.•Comprehensive analysis of volatile compounds by Flash GC E-nose and HS-GC-MS.•Critical compounds for tracing the geographical origins of ZSS were identified. Ziziphi Spinosae Semen (ZSS), a valuable seed food, has faced increasing authenticity issues. In this study, the adulterants and geographical origins of ZSS were successfully identified by electronic eye, flash gas chromatography electronic nose (Flash GC e-nose) and headspace gas chromatography-mass spectrometry (HS-GC-MS). As a result, there were color differences between ZSS and adulterants, mainly represented by the a* value of ZSS was less than adulterants. In ZSS, 29 and 32 compounds were detected by Flash GC e-nose and HS-GC-MS. Spicy, sweety, fruity and herbal were the main flavor of ZSS. Five compounds were determined to be responsible for flavor differences between different geographical origins. In the HS-GC-MS analysis, the relative content of Hexanoic acid was the highest in ZSS from Hebei and Shandong, while 2,4-Decadien-1-ol was the highest in Shaanxi. Overall, this study provided a meaningful strategy for addressing authenticity problems of ZSS and other seed foods.