Turbofan engine compressor is most severely threatened by the entry of liquid water during flight descent. This study aims to deeply understand the fluctuations of compressor performance parameters caused by water ingestion through frequency spectrum analysis. The water content and droplet diameter distribution are determined based on the real heavy rain environment. Results reveal that most of the droplets actually entering the core compressor have a particle size of less than 100 μm. In addition, the formation and motion of water film plays a critical role in affecting the fluctuation characteristics. Water ingestion deteriorates the compression performance and aggravates the unsteady fluctuations of the fan. However, the performance of the core compressor is less affected by water ingestion, but their fluctuations are still exacerbated. For some important parameters, such as inlet mass flow rate, total pressure ratio, total temperature ratio, compression work and efficiency, their main frequency of fluctuation are switched from the original blade passing frequency to the rotor passing frequency, and their amplitudes are correspondingly amplified to varying degrees. These phenomena can be observed in both the fluctuations of the fan and core compressor. Moreover, the operating point of them will be in the long-period and large-amplitude fluctuations, which leads them experiences the non-optimal state for a long time and threatens their operating stability.