This work introduces deformable slice-to-volume registration (DSVR) integrated into super-resolution reconstruction framework for correction of respiratory motion MRI. Using the initial estimation of respiratory motion as an input this method allows reconstruction of high-resolution volumes for specific respiratory positions using all slices. Based on diffeomorphic free-form deformation model, DSVR provides robust registration of deformable objects as well as out-of-plane motion correction. The feasibility of the method was successfully evaluated on a ‘motion-corrupted’ phantom and a free-breathing in-utero MRI scan. The results also indicated that the accuracy of spatial features in reconstructed volume is directly defined by the initial motion estimation.