The population is now more aware of their diets due to the connection between food and general health. Onions (Allium cepaL.), common vegetables that are minimally processed and grown locally, are known for their health-promoting properties. The organosulfur compounds present in onions have powerful antioxidant properties and may decrease the likelihood of developing certain disorders. It is vital to employ an optimum approach with the best qualities for studying the target compounds to undertake a thorough analysis of these compounds. In this study, the use of a direct thermal desorption–gas chromatography–mass spectrometry method with a Box–Behnken design and multi-response optimization is proposed. Direct thermal desorption is an environmentally friendly technique that eliminates the use of solvents and requires no prior preparation of the sample. To the author’s knowledge, this methodology has not been previously used to study the organosulfur compounds in onions. Likewise, the optimal conditions for pre-extraction and post-analysis of organosulfur compounds were as follows: 46 mg of onion in the tube, a desorption heat of 205 °C for 960 s, and a trap heat of 267 °C for 180 s. The repeatability and intermediate precision of the method were evaluated by conducting 27 tests over three consecutive days. The results obtained for all compounds studied revealed CV values ranging from 1.8% to 9.9%. The major compound reported in onions was 2,4-dimethyl-thiophene, representing 19.4% of the total area of sulfur compounds. The propanethial S-oxide, the principal compound responsible for the tear factor, accounted for 4.5% of the total area.