Distribution of volatile compounds in different fruit structures were analyzed in four tomato cultivars by headspace-solid-phase microextraction (SPME)-gas chromatography-mass spectrometry (GC-MS). A total of 36 volatile compounds were identified in fruit samples, which were primarily aldehydes, hydrocarbons, alcohols, ketones, furans, esters, nitrogen compounds, and sulfur and nitrogen-containing heterocyclic compounds. The volatile compositions in pericarp (PE), septa and columella (SC), locular gel and seeds (LS), and stem end (SE) tissues showed different profiles. The PE tissue showed the highest total volatile concentration due to a high abundance of aldehydes, especially cis-3-hexenal and benzaldehyde. Meanwhile, it showed higher aromatic proportion and herbaceous series intensity than other tissues. Floral and fruity series showed higher intensity in SC and LS tissues. The concentration of alcohols in the LS was higher than that in other tissues in association with the higher abundances of 2-methyl propanol, 3-methyl butanol, and 2-methyl butanol. However, the numbers and concentrations of volatile compounds, especially cis-3-hexenal, benzaldehyde, and geranyl acetone were lower in SE than in the other tissues, indicating less tomato aromas in SE. SE tissues were also lacking in floral and fruity characteristic compounds, such as geranyl acetone, 1-nitro-pentane, and 1-nitro-2-phenylethane. “FL 47” contained more volatile compounds than the other three, and the contents of aldehydes, ketones and oxygen-containing heterocyclic compounds in the “Tygress” fruit were higher than the other cultivars.