Recently, membrane distillation (MD) processes using two-dimensional graphene oxide (GO) membranes exhibited good light water/deuteriated water (H2O/D2O) separation performance, which depended on membrane materials and structures. This raises the need for the development of novel membrane materials and revealing the relationship of membrane structure-separation performance to further increase the separation performance. Here, one-dimensional (1D) MWCNT-based membrane was explored for the separation of H2O/D2O using the water source with specially chosen concentration of D in air–gap membrane distillation processes, and the resultant MWCNT membrane gave lower permeation flux and similar separation factor compared with the pristine GO membrane. Then GO-MWCNT composite membranes with different structure obtained by mixing various weight ratios of GO: MWCNTs were investigated, and their separation performance was found to be related with membrane structures. The resultant 3D hierarchy GO-MWCNT composite membrane (G/M−1:3) gave the highest permeation flux of 0.947 L·m−2·h−1 among all GO-MWCNT composite membranes, higher than that of the pristine GO membrane, while the separation factor of G/M−1:3 (1.045) and the pristine GO membrane (1.046) was comparable. Furthermore, the correlation of membrane structure-separation performance was reviewed. These results demonstrate the first example of MWCNT membrane and related composite membranes for H2O/D2O separation and suggest that H2O/D2O separation performance in membrane distillation processes can be improved by tailoring the structure of GO-MWCNT composite membranes. As the separation of H2O/D2O is usually used as a model in the laboratory for light water/tritiated water (H2O/HTO) separation process, this approach can guide for developing novel membrane materials and structures to deliver appropriate H2O/HTO separation processes needed in the nuclear energy field.