The application of organic fertilizers is one of the most important agricultural measures aimed at improving the flavor and productivity of Lycopersicon esculentum, with the granulation and coating of organic fertilizers, which can reduce seepage losses of great significance to the ecosystem. In this study, Jingcai 8 tomato was selected as the test material. Headspace solid-phase microextraction and gas chromatography–mass spectrometry (HS-SPME-GC-MS) methods were used to investigate the effects of different pelletized organic fertilizers and various coating materials on the flavor profile of the tomatoes. The results indicated that 67 volatile organic compounds (VOCs) were identified in the tomato fruits and 62 volatile compounds were identified in the leaves under different fertilizer treatments. The volatile compound content of the fruits in the BP treatment group was 35.38 μg/g, which was higher than that in other treatment groups, and the volatile compound content of the leaves was lower. A differential compound analysis with log2|fold change| ≥ 1 and variable important in projection (VIP) > 1 highlighted styrene, 3-methyl-1-butanol, and (E, E)-2,4-hexadienal as the major up-regulated compounds and methyl salicylate as the major down-regulated compound in the tomato fruit BCK (control) vs. BP.