Huajiao (Zanthoxylum bungeanum Maxim.) is extensively cultivated in various countries, including China, Korea, and India, owing to its adaptability to diverse environments. This study comprehensively analyzed the volatile substance composition of 14 varieties of red huajiao with distinct geographical origins. Thermal analysis methods, gas chromatography‐mass spectrometry (GC‐MS), and headspace‐ion mobility chromatography (HS‐IMS) were employed to evaluate the total volatile substance composition and content. The study revealed minor variations in water content, volatile matter content, and fractions among the geographically sourced huajiao samples. Utilizing correlation analysis based on GC‐MS and orthogonal partial least squares discriminant analysis (OPLS‐DA) with HS‐IMS, a robust classification method for the 14 types of huajiao was developed. Applying the variable importance in the projection (VIP) method, seven distinctive components were identified as potential markers for distinguishing the geographical origins of red huajiao. By integrating climatic and topographical factors of the 14 huajiao varieties, the correlation analysis of GC‐MS, and OPLS‐DA classification outcomes from HS‐IMS elucidated the influence of geo‐environmental factors on huajiao components and contents. This research provides insights into the impact of diverse geographic environments on the constituents and characteristics of huajiao. It offers valuable guidance for selecting optimal cultivation locations to enhance huajiao quality, aiding consumers in making informed choices.