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To<strong> </strong>compare the chemical differences between the medicinal and<em> </em>cultured oyster shells, their chemical profiles were investigated. Using the ultra performance liquid chromatography-electron spraying ionization-mass spectrometry (UPLC-ESI-MS), combined with principal component analysis (PCA) and orthogonal projection to latent structures discriminant analysis (OPLS-DA), the discrimination of the chemical characteristics among the medicinal and cultured oyster shells was established. Moreover, the chemometric analysis revealed some potential key compounds. After a large-scale extraction and isolation, one target key compound was unambiguously identified as caffeine (<strong>1</strong>) based on extensive spectroscopic data analysis (1D and 2D NMR, MS, and UV) and comparison with literature data.