We here perform an intercomparison of TFCT and IBM for large-eddy simulation of a turbulent wind field over a three-dimensional hill, for which wind-tunnel measurements are available for validation. The experimental dataset contains both vertical and horizontal profiles of mean velocities and variances, which allows an in-depth comparison of the numerical models. For the TFCT, a new algorithm for solving the pressure Poisson equation in the transformed coordinate system is proposed and first validated for a laminar flow over periodic two-dimensional hills by comparing with available benchmark solutions. Since the slopes of the three-dimensional hill are not steep, TFCT, which is free from implementation errors for the wall model, is preferable to IBM. The effects of sub-grid scale models and different schemes used to implement wall boundary conditions for IBM are studied. Discrepancies between the results obtained by TFCT and IBM are observed near the surface. The source of errors and possible ways to improve the IBM implementation are discussed.