This paper describes structural design of various polysiloxane-containing polymer membranes and their permselectivity for organic liquid mixtures in pervaporation. Morphology of microphase-separated membranes containing poly(dimethylsiloxane)(PDMS) strongly influenced their permselectivity in the separation of organic liquid mixtures. The analysis using various permeation models revealed that the continuity of the PDMS phase in the microphase separation governs the membrane permselectivity. This paper also focuses on simple surface modifications of polymer membranes by polymer additives and the their effects on the permselectivity for organic liquid mixtures. The permselectivity of the surface-modified membranes was controlled without lowering the permeability by the simple surface modifications. Introduction of calixarene and ionic liquids into polysiloxane-containing polymer membranes enhanced their permselectivity for organic liquid mixtures. In addition, liquid crystalline polysiloxane membranes underwent drastic changes in permeation and separation properties at their nematic-isotropic phase transition temperatures. Our results suggest novel concepts for structural design of polymer membranes, that is, methods for controlling and enhancing the permselectivity of polymer membranes without lowering their permeability.