The development and application of nuclear energy involves a challenging process of separating H2O/HTO to treat tritium-containing radioactive wastewater (HTO). Recently graphene oxide (GO)-based membrane distillation process has shown good performance for the separation of H2O/D2O used as a laboratory model research process for H2O/HTO separation, but further development of novel membrane materials or structures for membrane distillation process to give higher permeation flux or separation factor is still desirable. Here, boron nitride (BN) and molybdenum disulfide (MoS2) were investigated as membrane materials in the type of PTFE supported membrane, and PTFE/BN membrane showed higher permeation flux than PTFE/MoS2 and PTFE/GO membrane, and higher separation factor than PTFE/GO membrane that was higher than PTFE/MoS2 membrane. Furthermore, binary PTFE/BN/GO and PTFE/MoS2/GO heterostructure composite membranes were explored. The permeation flux of PTFE/BN/GO membrane was higher than that of PTFE/MoS2/GO and PTFE/GO/GO membrane. The separation factor of PTFE/BN/GO membrane was higher than that of PTFE/GO/GO membrane, which was higher than that of PTFE/MoS2/GO membrane. These results suggest that other 2D material- or heterostructure membranes can give performance comparable with or even better than GO membrane for the separation of H2O/D2O. This can guide for further exploration of novel materials or membrane structures for membrane distillation process with higher performance to provide a solution for the treatment of tritium-containing radioactive wastewater in the nuclear energy sector.