A comparable study were carried out by determination of trace elements on five marine-derived shell traditional Chinese medicine (TCM) (Ostreae Concha, Haliotidis Concha, Margaritifera Concha, Meretricis Concha, and Arcae Concha), which were recorded in the Chinese Pharmacopoeia (2010 version). Seven trace elements in 51 batches of this type of shell TCM were analyzed by Inductively Coupled Plasma Mass Spectrometry (ICP-MS), combined with principal component analysis (PCA) methods. The content of element Se, which exhibited significant differences among different drugs, could be used as a key element to distinguish this type of drugs. Meanwhile, the contents of elements Co, Cu, Mo, and Ba in Haliotidis Concha, Co and As in Margaritifera Concha, Mo and As in Meretricis Concha, Mo, As, and Ba in Arcae Concha, and Zn in Meretricis Concha were relatively stable. In the PCA plot, Arcae Concha and Meretricis Concha could be efficiently distinguished from Ostreae Concha together with Haliotidis Concha, and Margaritifera Concha. The results also showed a correlation with their medicinal function. In conclusion, trace elements in marine-derived shell TCM could not be neglected for their quality control.