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As a crucial component of water conservancy infrastructure and a core element of power equipment, the stability and reliability of the intake structure in large axial-flow pump systems (AFPS) play a pivotal role in ensuring the safety of water resource allocation projects, agricultural irrigation systems, and flood control and disaster mitigation efforts. Gaining a comprehensive understanding of the mechanisms underlying velocity distortion within the intake system, particularly the evolution of vortex patterns, is vital for mitigating hydraulic transient risks, improving flow structure stability, and preventing catastrophic failures in pump station engineering. This study systematically examines the instability mechanisms of the intake system caused by wall-attached vortices during the operation of AFPS, with an emphasis on flow uniformity, vortex position identification, and the extent of velocity distortion. Transient flow processes and velocity distributions in a large axial-flow pump system were numerically simulated using a three-dimensional volume of fluid + Level Set method to model intake flows at the pump system. The numerical simulation outcomes were validated against experimental data obtained from a model pump system. The spatiotemporal evolution of vortices was analyzed through advanced visualization techniques, and the instability phenomena induced by these vortices were assessed using velocity distribution uniformity tests and entropy production theory. Furthermore, key correlation factors influencing vortex generation and velocity distortion were identified, leading to the development of proactive strategies aimed at enhancing the safety and stability of the intake system.