In this study, balance equations of a binary mixture for molecular distillation were derived on the basis of the relation of heat and mass transfer in liquid films on both the evaporation and condensation surfaces. The effects of segmented condenser and evaporators on degree of evaporation, composition of condensate, surface temperature of evaporating and condensing film were studied. Results showed that influence of splashing on desired substance caused by insufficient removal of gases and re-evaporation were minimized by the segmented condenser. The component with larger mass concentration gradient of desired substance and increasement of evaporation degree were obtained. The temperature of evaporating film surface was increased through the rising temperature evaporation in segmented evaporator. The separation of mixtures with obvious different vapor pressures could be fulfilled and desired mass concentration of component could be obtained by the segmented evaporator.