Caffeic acid O-methyltransferase 1 (COMT1) is a key enzyme that is involved in melatonin synthesis, affecting the melatonin content in plants. In this experiment, tomato plants (slcomt1) with silenced SlCOMT1 gene expression were used to investigate the effects of SlCOMT1 deficiency on fruit growth, development, and quality formation. The results show that the slcomt1 plants exhibited prolonged fruit development, with reductions in the relative expression levels of SlCOMT1 by 71.1%, 79.7%, 83.9%, and 90.6% during the green fruit, breaker, orange ripening, and red ripening stages, respectively. The endogenous melatonin content also decreased by 29.4%, 43%, 45%, and 61.4% in the corresponding stages. Furthermore, the slcomt1 plants showed a decrease in the individual fruit weight, seed number per fruit, and fruit set rate by approximately 51.1%, 48.2%, and 30.4%, respectively. The slcomt1 plants exhibited an increase in the titratable acid content by 32.1%, 22.1%, 10.3%, and 24.4% during the green fruit, breaker, orange ripening, and red ripening stages, while the sugar-to-acid ratio decreased by 44.9%, 32.6%, 22.7%, and 36.8%. The slcomt1 plants also displayed increased fruit firmness, along with reductions in the relative expression levels of the cell wall and carotenoid-related genes and carotenoid content. Specifically, the Vc content in the slcomt1 plants decreased by 80.7% during the green fruit stage, and by 11.5%, 17.1%, and 2.6% during the breaker, orange ripening, and red ripening stages, respectively. The soluble protein content exhibited a decreasing trend in the corresponding stages. This study highlights the important role of endogenous melatonin in fruit physiology and quality formation, providing insights for further research and application of melatonin in agriculture.