Ultra-fine silicalite-1 particles were modified with four kinds of chlorosilanes (dodecyltrichlorosilane, octyltrichlorosilane, hexadecyltrichlorosilane and octadecyltrichlorosilane) and characterized by FI-IR, TGA, contact angle measurements and BET analysis. It was found that the surface hydrophobicity of silicalite-1 particles was improved significantly as the alkyl group was strongly bonded to the particle surface. Modified silicalite-1 particles were incorporated into PDMS (poly(dimethylsiloxanediol)) membranes, which were applied for the pervaporation separation of ethanol/water mixtures. The effect of surface properties, zeolite loading and operation conditions on pervaporation performance of the membranes was investigated. The separation factor of PDMS membranes filled with modified silicalite-1 increased considerably compared with that filled with unmodified ones, and the total flux decreased with increasing zeolite loading. The solution and diffusion selectivity of hybrid membranes were also measured to explain the pervaporation properties of silicalite-1 filled PDMS membranes. It was found that modification of silicalite-1 with dodecyltrichlorosilane effectively improved the solution and diffusion selectivity of silicalite-1 filled PDMS membranes with high zeolite loading. This may be attributed to the high surface hydrophobicity of modified silicalite-1 and its good integration with PDMS membranes. Both the high separation factor and solution selectivity indicated that modification of silicalite-1 with chlorosilanes was an effective method to improve the selectivity of silicalite-1/PDMS hybrid membranes for ethanol.