Rockfalls are major geological hazards threatening prestressed concrete cylinder pipes (PCCPs) in water diversion projects. To accurately assess the impact of large deformation movements of rockfalls on PCCPs, this study utilized the continuous–discontinuous method to investigate the dynamic response of a PCCP under a rockfall. The impact mode of rockfalls, the mechanical characteristics of PCCP, and the nonlinear-contact characteristics between soil and PCCP were considered in this study. The advantages of continuous and discontinuous numerical simulation methods were utilized to establish a continuous and discontinuous coupling model of “tube-soil-rock” considering the interaction of soil and structure. The impact mechanism and process of PCCP under the rockfall were investigated by simulating the rockfall process and analyzing its spatiotemporal evolution. The influence of PCCP under rockfalls with different heights and radii was studied to clarify the effects of these two parameters on the PCCP. Combined with a practical application example of large-scale water transfer projects, there is a tendency of center flattening under static load and dynamic impact load, and the PCCP part directly below the impact point is the most dangerous. This investigation provided a comprehensive understanding of the impact mechanism of the PCCPs under rockfall. The findings of this study have significant implications for the design of the protection engineering of PCCPs and ensuring the safe operation of water diversion projects.