Aiming at the problems of quality deterioration and flavor loss of fresh tomatoes after harvest, the effects of 4kJ/m² short-wave ultraviolet (UV-C) treatment on storage quality of fresh tomatoes was studied by using “original No. 1” fresh tomatoes as experimental materials. The results showed that compared with the control group, UV-C treatment effectively maintained the sensory quality of fresh tomatoes, delayed the decrease of firmness and total pectin content at the end of storage, decreased the content of malondialdehyde, and inhibited the activity of polygalacturonase at the early storage stage and pectin lyase at the late storage stage, consequently maintained the fruit texture. UV-C treatment slowed down the increase of weight loss rate, inhibited the decline of soluble solids, and increased the contents of total phenol and ascorbic acid at the late storage stage, thereby preserving the nutritional quality of fruit. A total of 44 volatile compounds were detected in two groups of fresh tomatoes during storage. UV-C treatment promoted the production of aroma substances, such as linalsol, cyclopentanone, (Z)-6-noneol and phenylacetaldehyde, while inhibited the decrease of characteristic aroma substances, such as 2-methyl-1-butanol, 2-methyltetrahydrofuran-3-one, phenylethanol and isobutyl isobutyrate, and the production of undesirable flavor substances such as propionic acid, 2-methyl-2-propanol, ethanol, 2-methylthiophene and 2-methylbutyrate. UV-C treatment could effectively maintain the quality of fresh tomatoes during storage, preserve their good flavor, and prolong the storage period. The research results aimed to provide theoretical reference for the application of UV-C irradiation technology in the preservation of fresh fruits and vegetables such as tomatoes.