Molecular dynamics simulations have now been broadly applied to investigate membrane transport and optimize membrane design, but mostly for nanostructures without the involvement of phase change due to the enormous computational time and spatial scale requirements. In the present study, a coarse-grained molecular dynamics model is developed to overcome the limitations in simulating membrane distillation through meso-size (2-5 nm) channels formed by graphene bilayer at the direct contact mode. The new coarse-grained approach enables the comprehensive evaluation of the influences of channel opening, hydrostatic pressure, and temperature. In addition, the evaporation processes at the membrane surface as well as the water vapour transport can now be analysed in a statistically reliable manner. The coarse-grained results show that the permeate flux through the graphene bilayer channels is almost three-order-of-magnitude higher than the commonly used microporous polymer membranes nowadays, which demonstrate the significant application potential. Increasing the hydrostatic pressure is found to be uneconomical due to its limited effects. The enhanced evaporation at small channel opening is due to the elevated collisions among the interface water molecules. Most importantly, the permeate flux shows a non-monotonic dependence on the channel opening. The flux is highest when the channel opening is 2 nm, after which the dominant transport of water molecules inside the channel transit from surface diffusion to activated Knudsen transport. This finding has an important implication towards the design of graphene bilayer membranes for membrane distillation in the future.