The turbulent flow over a channel bed roughened by three layers of closely packed spheres with a Reynolds number of Re=15000 is investigated using the large eddy simulation (LES) and the double-averaging (DA) method. The DA velocity is compared with the results of the corresponding laboratory experiments to validate the LES results. The existence of the types of vortex structures is demonstrated by the Q-criterion above the permeable bed. The turbulent kinetic energy (TKE) fluxes and budget are quantified and discussed. The results show that the TKE fluxes are directed downward and downstream near the virtual bed level. In the TKE budget, the form-induced diffusion rate is significant in the vicinity of the crest bed level, and the TKE production rate and the dissipation rate attain their peaks at the crest bed level and decrease sharply below it.