Hawthorn is a type of natural food with significant medicinal and nutritional properties; it has been listed in the “Both Food and Drug” list by the Chinese Ministry of Health Item List since 1997. However, hawthorn varieties have complex origins, and there are significant differences in the content, type, and medicinal efficacy of the chemically active ingredients in different varieties of hawthorn. This leads to the phenomenon of mixed varieties and substandard products being passed off as high-quality. In this work, by using headspace gas chromatography–ion mobility spectrometry (HS-GC-IMS), we identified and analyzed volatile organic compounds (VOCs) in four varieties of hawthorn, establishing their characteristic fingerprints. As a result, a total of 153 peaks were detected, and 139 VOCs were also identified. As shown by the fingerprint profiles, the different hawthorn samples contained different VOCs. Meanwhile, by using principal component analysis (PCA), Euclidean distance, and partial least-squares discriminant analysis (PLS-DA), the relationship between the VOCs found in the different varieties of hawthorn was revealed. This study developed a simple, fast, accurate, and sensitive method for identifying, tracking, and evaluating hawthorn varieties.