Objective To optimize the extracting technology of assessing the maximum yield of phenolic compounds (PC) from Inonotus obliquus by single factor experiments and orthogonal array design methods through aqueous two-phase systems combined with ultrasonic extraction. Methods The range of the independent variables, namely levels of acetone and ammonium sulfate, and ultrasonic time were identified by a first set of single factor experiments. The actual values of the independent variables coded at four levels and three factors were selected based on the results of the single factor experiments. Subsequently, the levels of acetone and ammonium sulfate, and ultrasonic time were optimized using the orthogonal array method. Results The optimum conditions for the extraction of PC were found to use 7.0 mL acetone, 5.5 mg ammonium sulfate, with ultrasonic time for 5 min. Under these optimized conditions, the experimental maximum yield of PC was 37.8 mg/g, much higher than that of the traditional ultrasonic extraction (UE, 29.0 mg/g). And the PC obtained by this method had stronger anti-oxidative activities than those by traditional UE method. Conclusion These results indicate the suitability of the models developed and the success in optimizing the extraction conditions. This is an economical and efficient method for extracting polyphenols from I. obliquus.