3D interleaved DW-EPI with 2D multiplexed sensitivity encoding has been shown useful in achieving submillimeter DTI. Similar to other 3D DTI techniques, 2D phase variation is only considered in eliminating aliasing artifacts, thereby limiting feasible slab thickness. 3D phase correction is a potential strategy to significantly improve the image quality and feasible slab thickness of 3D DTI. To enable 3D phase correction, we develop a new reconstruction algorithm, and implement an EVI-based navigator echo for direct 3D phase measurement. Quantitative results show that the proposed algorithm can effectively eliminate aliasing artifacts and signal corruptions due to 3D inter-shot phase variations.