Tomato (), a leading vegetable crop of significant economic importance, is a valuable source of nutrients and minerals in the human diet. Consumer and breeder interest focuses extensively on tomato quality attributes, including appearance, texture, flavor, and nutritional value. While moderate low temperatures are generally beneficial for preserving tomato quality during transportation and storage, the precise effects of storage temperature on these qualities remain to be fully elucidated. This study investigated the changes in quality attributes of tomato (cv. Shangjiao No.2) fruit stored at different temperatures (4 °C, 14 °C, and 24 °C) for varying durations (0, 1, 5, 9, and 15 days postharvest, dph). Results showed that low temperatures (4 °C and 14 °C) were beneficial for maintaining fruit appearance and total soluble solids (TSS) content. Furthermore, 4 °C storage effectively delayed ascorbic acid (Vitamin C) loss. Storage at both 4 °C and 14 °C similarly and significantly reduced fruit softening and water loss rate (WLR). This reduction was associated with the temperature-regulated expression of cell wall-related genes, including , , , and . The activities of cell wall-degrading enzymes, such as polygalacturonase (PG), β-galactosidase (β-Gal), and cellulase, were also significantly inhibited at lower storage temperatures. Additionally, storage at 24 °C caused considerable damage to plastid ultrastructure. Although temperature had a minor effect on carotenoid, the reduction in carotenoid levels was less pronounced at 4 °C. While low-temperature storage suppressed the release of some aroma compounds, it also reduced the levels of undesirable volatiles. This study provides insights for optimizing storage temperature and duration to maintain tomato fruit quality.