For medical cone-beam computed tomography (CBCT) imaging, the native receptor array of the flat-panel detector (FPD) is usually binned into a reduced matrix size. By doing so, the signal readout speed can be increased by over 4-9 times at the expense of sacrificing the spatial resolution by at least 50%-67%. Clearly, such tradition poses a main bottleneck in generating high spatial resolution and high temporal resolution CBCT images at the same time. In addition, the conventional FPD is also difficult in generating dual-energy CBCT images. In this paper, we propose an innovative super resolution dual-energy CBCT imaging method, named as suRi, based on dual-layer FPD (DL-FPD) to overcome these aforementioned difficulties at once. With suRi, specifically, an 1D or 2D sub-pixel (half pixel in this study) shifted binning is applied to replace the conventionally aligned binning to double the spatial sampling rate during the dual-energy data acquisition. As a result, the suRi approach provides a new strategy to enable high signal readout speed and high spatial resolution CBCT imaging with FPD. Moreover, a penalized likelihood material decomposition algorithm is developed to directly reconstruct the high resolution bases from the dual-energy CBCT projections containing spatial sub-pixel shifts. Experiments based on the single-layer FPD and DL-FPD are performed with physical phantoms and biological specimen to validate this newly developed suRi method.The synthesized monochromatic CT imaging results demonstrate that suRi can significantly improve the spatial image resolution by 46.15%. We believe the developed suRi method would be capable to greatly enhance the imaging performance of the DL-FPD based dual-energy CBCT systems in future.