Oral ulcers, a common mucosal affliction, severely diminish patients' quality of life due to pain and discomfort. Despite existing treatments, the frequent recurrence of oral ulcers underscores the need for more effective therapeutic options. This study aimed to investigate the inhibitory effects of Ponkan (Citrus reticulata 'Ponkan') extracts and their flavonoid components on oral ulcers, exploring their potential as a natural therapy. Twenty different Ponkan cultivars were selected for flavonoid extraction and analysis. Ultra-performance liquid chromatography (UPLC) and high-resolution mass spectrometry (HRMS) were utilized for substance identification, leading to the discovery of 16 flavonoid compounds. Using an oral ulcer model established in Wistar rats, Ponkan extracts were found to effectively reduce ulcer area and pain sensitivity. The study revealed that four polymethoxyflavones (PMFs) were particularly effective in treating oral ulcers, while hesperidin did not show significant improvement. Mechanistic studies indicated that PMFs could inhibit the phosphorylation of Jak2 and Stat3, whereas hesperidin lacked this effect. This research supports the potential use of Ponkan and its flavonoids as a natural and effective alternative therapy for oral ulcers, with a focus on the role of PMFs in modulating the Jak2-Stat3 pathway, highlighting the possibilities for targeted natural treatments.