Solanum habrochaites, an important tomato germplasm resource, is resistant to multiple insect pests and produces an array of secondary metabolites on the leaf surface. We used gas chromatography-mass spectrometry (GC-MS) to determine the secondary metabolites on the leaf surface of 4 tomato accessions: one S. lycopersicum 9706 and 3 S. habrochaites accessions LA1777, LA2329 and PI134417. The 3 S. habrochaites accessions produced high amounts of secondary metabolites, whereas S. lycopersicum 9706 lacked most of these secondary metabolites. Secondary metabolites on the 9706 leaf surface were 6 terpenoids, which included 3 monoterpenes and 3 sesquiterpenes, of 60.3% and 39.7%, respectively. LA2329 and LA1777 accumulated high amounts of sesquiterpenoids, but the types of sesquiterpenes differed between accessions. α-zingiberene was the most abundant sesquiterpene (2 409.1 μg·g^–1) in LA2329. γ-Elemene and E-β-farnesene were the major sesquiterpenes in LA1777: 573.3 and 289.9 μg·g^–1, respectively. Dodecanoic acid ethenyl ester, at 5 312.8 μg·g^–1, was the most abundant secondary metabolite in PI134417. This metabolite has not previously been reported in any tomato species. In addition, methyl ketones, specifically 2-undecanone and 2-tridecanone, at 689.8 and 1 459.7 μg·g^–1, respectively, were abundant secondary metabolites in PI134417. Our study provides the theoretical basis for the use of tomato germplasm resources and the development of secondary metabolites.