Image registration for X-ray dual energy imaging is challenging due to the overlaid transparent layers (i.e., the bone and soft tissue) and the different appearances between the dual images acquired with X-rays at different energy spectra. Moreover, subpixel accuracy is necessary for good reconstruction of the bone and soft-tissue layers. This paper addresses these problems with a novel coupled Bayesian framework, in which the registration and reconstruction can effectively reinforce each other. With the reconstruction results, we can design accurate matching criteria for aligning the dual images, instead of treating them as multi-modality registration. Furthermore, prior knowledge of the bone and soft tissue can be exploited to detect poor reconstruction due to inaccurate registration; and hence correct registration errors in the coupled framework. A multiscale freeform registration algorithm is implemented to achieve subpixel registration accuracy. Promising results are obtained in the experiments.