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 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 deuterium (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 structures obtained by mixing various weight ratios of GO: MWCNTs were investigated, and their separation performance was found to be related with membrane structures. The resulted 3D hierarchical 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.