For a pre-swirl pump-jet propulsor (PJP), the stator inevitably induces the problem of rotor–stator interaction (RSI). In this paper, the mechanism of RSI in a PJP is analyzed through dynamic mode decomposition (DMD). The coherent flow structures and corresponding frequencies have been decomposed and analyzed. The results show that the dominant frequencies of pressure fluctuation in the stationary domain are BPF (rotor blade passing frequency) and its multiples. In contrast, the dominant frequencies in the rotational domain are SPF (stator passing frequency) and its multiples. The frequencies of k*SF (SF, shafting frequency; k = 4, 5, and 8) have also been found. The mode structure corresponding to the SPF is stable and has the highest mode energy. The reconstruction residual formula is introduced, and the axial velocity flow field is reconstructed well by the DMD modes compared with the raw flow field. This research can provide a reference for studying and suppressing RSI in a PJP.