A molecular dynamics simulation (MDS) technique is used to study the heat and mass transfer inside the composite PVDF (polyvinylidene fluoride)/SiO2 (Si aerogel) bilayer membrane at molecular level. The reverse non-equilibrium molecular dynamics (RNEMD) simulation method is employed to determine the thermal conductivity at each layer and at the interface. Moisture diffusivity is also modeled by the mean square displacements (MSD) of water vapor in the materials. In combination with macro scale resistance models for porous media, the heat conductivity and moisture diffusivity through the whole membrane are calculated. It is found that the interface has a great influence on the membrane overall resistance, especially for thinner membranes. Molecular groups can be manipulated to adjust this resistance. When the hydroxyl groups are increased from 58% to 100%, the membrane overall heat conductivity can be increased by 57%, and the diffusivity can be increased by 48%. The fractional free volume, vibrational density of states (VDOS), adhesion energy, thermal and moisture resistance in each layer and at the interface are investigated to disclose the transport mechanisms. Membranes of low conductivity and high moisture diffusivity that are desired for air humidification applications can be obtained by such molecular level manipulations. By this work, a multi-scale model for interfacial heat and mass transfer resistance between two contacting materials, that considers both macro-scale roughness and porosity and micro-scale molecular interacting, is provided.