This study aimed to compare the flavonoid accumulation between ozone-treated and untreated Satsuma mandarin (Citrus unshiu Marc.) fruits. The fruits exposed to gaseous ozone were found to have higher antioxidant activities and content of flavonoid during the storage period by ultra-high performance liquid chromatography (UPLC). To reveal the molecular regulation of flavonoid accumulation by ozone, chalcone synthase (CHS), chalcone isomerase (CHI), β-1,3-glucanase (GLU), chitinase (CHT), phenylalanine ammonia-lyase (PAL), and peroxidase (POD) were identified and their expression was examined by quantitative real-time polymerase chain reaction (q-PCR). These results support the promising application of ozone treatment as a safe food preservation technique for controlling postharvest disease and extending shelf-life of harvested Satsuma mandarin.