Multi-shot EPI technique is vulnerable to patient motion. Though CIRIS proposed by our group tackles the infrequent macroscopic motion in multi-shot EPI by clustering and registration, it cannot deal with the frequent motion (e.g. shot-wise motion). In this work, an iterative motion compensation frame was introduced to correct for the frequent motion during the multi-shot acquisition. The simulation experiments demonstrated that the proposed method can obtain improved image quality in the presence of infrequent motion, and even correct for the shot-wise motion, compared to CIRIS.