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<i>Zanthoxylum</i> plants, important aromatic plants, have attracted considerable attention in the food, pharmacological, and industrial fields because of their potential health benefits, and they are easily accessible because of the wild distribution in most parts of China. The chemical components vary with inter and intraspecific variations, ontogenic variations, and climate and soil conditions in compositions and contents. To classify the relationships between different <i>Zanthoxylum</i> species and to determine the key factors that influence geographical variations in the main components of the plant, the fatty acid composition and content of 72 pericarp samples from 12 cultivation regions were measured and evaluated. Four fatty acids, palmitic acid (21.33–125.03 mg/g), oleic acid (10.66–181.37 mg/g), linoleic acid (21.98–305.32 mg/g), and linolenic acid (0.06–218.84 mg/g), were the most common fatty acid components in the <i>Zanthoxylum</i> pericarps. Fatty acid profiling of <i>Zanthoxylum</i> pericarps was significantly affected by <i>Zanthoxylum</i> species and geographical variations. Stearic acid and oleic acid in pericarps were typical fatty acids that distinguished <i>Zanthoxylum</i> species based on the result of discriminant analysis (DA). Palmitic acid, palmitoleic acid, trans-13-oleic acid, and linoleic acid were important differential indicators in distinguishing given <i>Zanthoxylum</i> pericarps based on the result of orthogonal partial least squares discriminant analysis (OPLS-DA). In different <i>Zanthoxylum</i> species, the geographical influence on fatty acid variations was diverse. This study provides information on how to classify the <i>Zanthoxylum</i> species based on pericarp fatty acid compositions and determines the key fatty acids used to classify the <i>Zanthoxylum</i> species.