Aurantii fructus (zhiqiao, ZQ) is a traditional Chinese medicine (TCM) and raw material of TCM healthcare food (TCM-HF), mainly focused on the regulation of gastrointestinal disorders and the abundant application of antioxidants. Pharmacological investigations of ZQ flavonoids have identified them as the main bioactive components in recent years, but little has been reported on the extraction processes of antioxidant flavonoids (AFs). The aim of this study was to establish an efficient ultrasonic-assisted extraction (UAE) method for the extraction of AFs from ZQ using a response surface methodology (RSM), analyze the composition of AFs, and develop a qualitative evaluation method for ZQ. Flavonoid yield and antioxidant ability were selected as the responses to optimize the extraction of AFs, and the multiple effects of independent variables were investigated. The optimized conditions for the extraction of AFs based on the Box-Behnken design (BBD) were as follows: ethanol concentration, 58%; extraction temperature, 70 °C; and extraction time, 17 min. The flavonoid yield and antioxidant activity reached 241.70 mg/g and 59.42%, respectively, which matched the predicted values. Furthermore, optimized UAE processes were first established for the efficient and fast extraction of AFs. Flavanones and polymethoxyflavonoids (PMFs) were identified as potential AFs using time-of-flight mass spectrometry. Meanwhile, the quality of ZQ was evaluated using the criteria importance through intercriteria correlation (CRITIC) method for the first time, and Yuanjiang ZQ was considered as an excellent raw material of TCM-HF.