Large eddy simulation (LES) was performed for flow and heat transfer under stable density stratification in a wavy wall channel. Low-Mach-number approximation was applied to treat the effects of density variation. A mixed-time-scale (MTS) model was used as a subgrid-scale (SGS) model. The numerical results at four grid resolutions were compared with existing data of numerical experiments, and revealed that the grid dependency of the SGS model in stably stratified flow is quite larger than that in neutral flow. Flow becoming stably stratified, the flow pattern and the instantaneous turbulent structures near the wavy surface did not markedly change, whereas the intensity of turbulence considerably decreased between the wavy surface and the center of the channel. The budgets of turbulent energy and Reynolds stresses suggested that energy transports between Reynolds normal stresses are activated far from the wavy surface, and spatial transports of turbulence are suppressed near the surface under stable stratification.