Boundary layer ingestion (BLI) propulsion can improve aircraft aerodynamic efficiency, but also introduces inlet distortion that affects fan flow and stability. This study investigates the resulting unsteady flow response and loss mechanisms by performing a parallel comparison of unsteady Reynolds-averaged Navier–Stokes (URANS) and large-eddy simulation (LES) under unified geometry and boundary conditions, together with a time-sequence analysis of three representative LES instants. The results show that, compared with URANS, LES provides a more detailed depiction of the distortion pattern and internal vortical structures. LES captures the generation and mixing of fragmented vortex systems, and reveals corner separation near the stator hub and the decay of throughflow capacity, identifying major internal loss sources. The time-sequence comparison further shows that, although the distorted vortex core evolves in strength and shape, its circumferential phase remains essentially preserved, leading to a stable distorted sector at the aerodynamic interface plane. Within this sector, the rotor approaches critical incidence and triggers local separation, while the stator passages exhibit a sector-fixed, circumferentially continuous loss distribution. These findings clarify distortion-induced unsteady loss mechanisms in BLI fans and provide numerical guidance for locating loss regions and supporting distortion-tolerant design of intake–fan integrated systems.