Large-eddy simulation (LES) is performed to investigate the dynamics of flow and canopy motions and the energy transfer in turbulent canopy flows. Different from the traditional approach that models the canopy as a continuous medium with a drag coefficient prescribed a priori, an immersed boundary method together with a beam model is employed to explicitly capture the dynamics of individual stems and resolve monami. The simulation cases cover a broad range of stem flexibilities from rigid stems to oscillatory stems to stems yielding to the flow. For highly flexible canopies, the stem fluctuation is small such that the canopy behaves like a rigid canopy, which is used to explain the similarities of the flow features between rigid and highly flexible canopies. Analyses of the turbulent kinetic energy (TKE) budget show that, in the flexible canopy cases, the waving term associated with the canopy drag–flow velocity correlation can be as large as one-half of the shear production term near the canopy top. Spectral TKE budget analyses further reveal dominant effects at two characteristic scales: the monami scale associated with the coherent structures in the mixing layer and the wake scale associated with the interval between adjacent stems. For the TKE in flexible canopies, the waving term is found to play an important role in the interscale and wall-normal transport terms. Our LES data show that the spectral shortcut mechanism proposed by previous studies is caused by the waving term.