This study constructs and validates a high-efficiency and high-fidelity adaptive Very Large Eddy Simulation (VLES) strategy based on user defined function(UDF) secondary development to investigate the complex and unsteady flow characteristics of civil aircraft intakes under crosswind conditions, conducting a comparative study of turbulence simulation methods across different hierarchies. Initially, the performance of traditional RANS turbulence models, including S-A, BSL k-ω, and SST k-ω, in simulating large-scale flow separation within intakes under crosswind conditions is evaluated, revealing that their applicability is limited. However, the predictive accuracy of RANS models can be improved to some extent by incorporating Explicit Algebraic Reynolds Stress Models (EARSM) and non-linear constitutive corrections. Under the maximum crosswind mass-flow condition, for complex flows dominated by shock and boundary-layer interaction, the SST model, high-resolution Large Eddy Simulation (LES), and the developed VLES model are compared. Furthermore, under variable crosswind mass-flow conditions, a comparative study on separation characteristics between the VLES and SST models is carried out. Finally, the simulation performance of the VLES model under installed nacelle conditions is verified. Research results indicate that the VLES model achieves superior near-wall boundary layer resolution while effectively mitigating the over-prediction of separation zone extent typically associated with LES, demonstrating higher accuracy without a significant increase in computational cost. Through verification via independent nacelle calculations, the VLES method shows a high degree of consistency with experimental data and non-linear SST model results in predicting separation characteristics under varying mass-flow rates, accurately reproducing the processes of shock-induced separation and boundary-layer reattachment. This research establishes the superiority of the VLES method in handling complex intake flow separation, laying a theoretical and technical foundation for its engineering application in the aerodynamic assessment of actual installed nacelles.