Volatile components are one key factor in sample identification, differential analysis, quality control and origin traceability. In order to identify and analyze the differences in volatile substances in different alfalfa seeds, this study used gas chromatography–ion mobility spectrometry (GC-IMS), combined with the Gallery Plot plug-in, and PCA, PLS-DA and other analysis methods. In this way, a comprehensive analysis of volatile components in 10 alfalfa seeds, including aerospace varieties, was conducted. A comparative analysis of the characteristics of different sample compounds using topographic maps and fingerprints led to isolation of 48 kinds of 54 volatile compounds. Among them, esters (9 types), olefins (8 types), ketones (8 types), alcohols (6 types) and aldehydes (6 types) were found to be the most abundant volatile compounds in alfalfa seeds. At the same time, PCA and PLS-DA analysis models showed that esters, ketones and alcohols were the main volatiles causing the differences among alfalfa seeds. Among them, the content of various substances in the ZT2 and ZT3 aerospace varieties were higher than that of other varieties, while the types and contents of volatiles in ZT1, ZM2 and GN3 were relatively low. Therefore, in combination with the differences in maturity of each sample, the 10 varieties of alfalfa were finally divided into three categories, and the varieties of the same series were basically classified into one category. This provides a basis and convenience for future seed screening, identification, traceability and forage breeding.