In this study, the nutritional values and volatile components of Shenxian beans sterilized via two different methods (high temperature and microwave) were analyzed by the national standard method, head-space solid phase micro-extraction (HS-SPME), and gas chromatography-mass spectrometry (GC-MS). A total of 95 compounds were identified and classified into nine major groups. The major classes of compounds included alcohols (26), hydrocarbons (21), aldehydes (18), ketones (5), acids (5), phenols (4), esters (4), ethers (3), and nitrogenous (9). The volatile components in Shenxian beans could be affected by the sterilization method. The relative content of alcohols and ketones increased significantly, while those of ethers, aldehydes, phenols, and nitrogenous decreased, and those of acids, esters, and hydrocarbons did not obviously change owing to high temperature and microwave sterilization. Furthermore, both sterilization methods contributed to the increase in the total free amino acid (FAA) content, especially the total umami amino acid content in Shenxian beans. Shenxian beans treated with microwave sterilization had a better quality than those treated with high temperature sterilization.