The elimination of possible defects is indispensable in making zeolite membranes popular in process industries. A novel counter-diffusion chemical liquid deposition (CLD) technique is proposed and developed for selective defect-patching of zeolite membranes. Dodecyltrimethoxysilane (DMS) is employed as the silane coupling agent, forming a protective layer on the membrane surface so that intracrystalline pores can be kept intact in the subsequent reparation step. By using tetraethoxy orthosilicate (TEOS) and (3-chloropropyl)triethoxysilane (3CP-TES), co-hydrolysis and co-condensation at the organic/aqueous interface fabricate the silsesquioxane/silicate hybrid on macro-, meso- and even microdefects. The silicalite-1 membrane before and after reparation is characterized using contact-angle measurements, Fourier transform IR spectroscopy, and electron probe microanalysis. Permporometry is conducted to study the pore-size distribution of the membrane before and after reparation. It is found that the silsesquioxane/silicate hybrid is only deposited at the pore-mouth of the defects, and the defects can be plugged to less than 1.3 nm pores after patching. After reparation, the separation factor of a 50150 n/i-butane-gas mixture through the membrane can be increased to 35.8 from 4.4, and the separation factor of a CO2/N-2 gas mixture through the membrane can be increased to around 15 from 1, while keeping the two-thirds CO2 permeation flux of the synthesized membrane.