Synthetic aperture radar (SAR), as an active microwave remote sensor with high-resolution earth observation, is easily affected by radio frequency interference (RFI). Pulse radio frequency interference (PRFI), as a typical form of RFI, pollutes SAR raw data with bright stripes, which increases the difficulty of SAR image interpretation. However, the conventional eigen subspace projection (ESP) method decomposes the whole pulse into the interferences and the useful signals, resulting in the loss of useful signals in the non-interference positions with the pulse. To solve this problem, this paper proposes an improved SAR PRFI suppression method based on ESP. Firstly, the receiving pulses containing PRFI are detected and the specific position of PRFI in the pulse are determined by eigenvalue decomposition and energy accumulation in timefrequency domain, respectively. Secondly, the PRFI signal is separated from the useful signal by applying the ESP method only to the data where the PRFI is located. Finally, the PRFI signal projected by ESP is eliminated from the raw data. Simulation results shown that the proposed method can better protected useful signals and improve SAR image quality compared with conventional methods.