In performing molecular profiling of secondary metabolites, a lot of research has focused on biogenic volatile organic compounds with medium to low polarity. In this study, chemical composition similarity relationships among the various organs of the Ilex cornuta Lindl. & Paxton were assessed based on the analysis of hydrophilic volatile compounds. GC-MS analysis was conducted to characterize and classify the chemical compounds. A total of 36, 46, 42, 25, 64, 26 compounds have been respectively extracted from the root, stem, stem skin, leaf, flower and fruit. The six organs have 3 common compounds and large percentages of exclusive compounds ranging from 36.0% to 62.5% with a mean of 49.8%, indicating substantial component differences among the different organs. The percentage of overlapping compounds between each of the two organs ranges from 10.9% to 44.0%, which is relatively small, further demonstrating the strong organ specificity of the chemical composition. The overlapping index is used to reveal the similarity among the organs. The stem shares the maximum similarity while the fruit the minimum similarity with the other organs. Aside from fruit, the average overlapping indices between each of the other two organs correlate well to their physical proximity. In conclusion, hydrophilic volatile metabolites are a class of natural products that are rarely investigated but constitute a significant part of the plant chemical composition. Chemical profiling of these metabolites could provide a valuable tool for the plant taxonomy and help understand the chemically mediated biological phenomena.