Against the educational backdrop of deep interdisciplinary integration and empowering new models for cultivating composite talents， this innovative training experiment focuses on the hot interdisciplinary field of molecular archaeology， targeting the fragmented state of paleontological remains that do not have morphological identification characteristics and cannot be accurately identified for species. We developed a zooarchaeology by mass spectrometry （ZooMS） method based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry （MALDI-TOF MS）， utilizing collagen peptide mass fingerprinting （PMF）. This approach was successfully applied to species identification of late pleistocene fragmented paleontological samples. ZooMS offers significant advantages including operational simplicity， high identification accuracy， broad applicability， low testing costs， high-throughput analysis and stringent contamination control， making it highly valuable for species identification and the extraction of “hidden information” from fragmented paleontological remains. Through this innovation training experiment， we enhanced interdisciplinary collaboration between humanities and sciences， stimulated students’ scientific thinking， and improved their research competencies， laying a solid foundation for cultivating interdisciplinary and innovative talents.