This study aimed to establish a method for the simultaneous determination of isoquercitrin, trifolin and afzelin in A. persica flowers by high performance liquid chromatography (HPLC) with ionic liquid as extractant and ultrasonic-assisted extraction. The effects of ionic liquid concentration, solid–liquid ratio, number of crushing mesh, ultrasonic time, extraction temperature, and ultrasonic power on the extraction yield of three target compounds were investigated using the extraction yield of target analytes as the index. According to the results of single factor experiment, the Box-Behnken design-response surface methodology (BBD) was used to optimize the extraction method and compared with the traditional extraction method. The results showed that, calibration curves had excellent linearity (R2 > 0.9990) within the test ranges. In combination with other validation data, this method demonstrated good reliability and sensitivity, and can be conveniently used for the quantification of isoquercitrin, trifolin and afzelinin A. persica flowers. And the contents of isoquercitrin, trifolin and afzelin were 64.08, 20.55 and 75.63 μg/g, respectively. The optimal process obtained by BBD was as follows: ionic liquid concentration was 1.0 mol/L, solid–liquid ratio was 1:40 g/ml, mesh sieve was 50 mesh, ultrasonic time was 40 min, extraction temperature was 50 °C, and ultrasonic power was 400 W. Under the optimal conditions, the theoretical predicted total extraction yield of the three target compounds was 159.77 μg/g, which was close to the actual extraction value (160.26 μg/g, n = 3), this result indicating that the optimal process parameters obtained by response surface methodology analysis were accurate and reliable. The method was simple, accurate and rapid for determination the contents of three active ingredients in A. persica flowers.