Allium vegetables attract attention for their flavor and aroma in Asia, especially in China and Japan. The aim of this experiment was to uncover the differences in the unique flavor compounds of two Welsh onions that are typical cultivars in China and Japan (‘Zhangqiu’ and ‘Tenko’). Chemical methods and solid-phase microextraction–gas chromatography-mass spectrometry were performed to determine the nutritional quality and quantity of volatile compounds of various organs of Welsh onions. The results show that a total of 30, 37, and 28 compounds were detected in the roots, pseudostem, and leaves of ‘Zhangqiu’, respectively, while 21, 27, and 20 compounds were detected in the corresponding organs of ‘Tenko’. The distribution of sulfur compounds in the roots, pseudostem, and leaves of ‘Zhangqiu’ accounted for 72%, 83%, and 26% of the total content, while those of ‘Tenko’ accounted for 55%, 84%, and 57%, respectively. Aldehydes are the second largest class of volatiles in Welsh onions. The distribution of aldehydes in the leaves was notably different: 52% and 27% in ‘Zhangqiu’ and ‘Tenko’, respectively. The contribution of S to the volatile substances was outstanding, and through forward selection, it was found that P, Ca, and Mg contribute to the volatile substances of Welsh onions. The above results indicate that the different genotypes of Welsh onions have various flavors, and mineral elements contribute variously to these flavors. Calcium could be a new topic of interest for our subsequent research on elements and volatiles.