As the dramatic advancement in array signal processing, the phase array radar becomes widely used in military. However, the electromagnetic environment is very complicated with different kinds of electromagnetic interference. It makes the expected signal very difficult to be accurately received. The adaptive interference suppression method is adopted in the phase array radar to suppress the different kinds of interference. But this method works well only if the interference is the sidelobe interference. In this paper, we propose a two layer adaptive monopulse method to suppress the mainlobe and sidelobe interference. The main idea is to divide the mainlobe interference suppression and sidelobe interference suppression into two layers. First, the mainlobe maintains the same when performing sidelobe interference suppression. Then, the mainlobe interference is suppressed at the pitch and azimuth while the monopulse ratio stays unchanged. The simulation results show that our proposed method has good performance in estimation of the direction of arrival and interference suppression.