Introduction: Chaenomeles sinensis and C. speciosa are two closely related plant species. The confusion or adulteration between the two species is a common occurrence in the herbal market. Method: A specific TLC method was established to distinguish C. speciosa from C. sinensis. Furthermore, a new UPLC-Orbitrap-MS/MS method was developed for their classification. This method entailed analyzing massive MS data from Chaenomeles species, which were processed using a self-designed VBA program. The classification was facilitated by three chemometric approaches. Results: 3-O-Acetylursolic acid was discovered, separated, and identified from C. speciosa as the unique chemical marker. A TLC identification test was thus established to discriminate between these two species using this marker. All three chemometric models demonstrated robust classification of 20 Chaenomeles samples. Subsequent structural profiling of chemical compositions in Chaenomeles species was accomplished. Discussion: Most of the identified compounds included triterpenoids, with nine compounds common to both species. TLC and UPLC-MS/MS methods were established for differentiating C. speciosa from C. sinensis. Conclusion: The present study also introduces an integrated analytical workflow that merges rapid TLC prescreening with high-resolution UPLC-MS/MS fingerprinting and chemometric modelling, enabling unequivocal discrimination of phylogenetically proximate plant species.