The improvement of sodium ions added in the synthesis solution is verified for fabrication of high quality pure silica MFI zeolite membranes. The effects of sodium ions on separation performance, growth and hydrophobicity of MFI membranes are thoroughly characterized by scanning electron microscopy (SEM), X-ray diffraction (XRD), energy dispersive X-ray (EDX) spectroscopy, infrared (IR) spectra, thermogravimetric (TG) analysis, water contact angle test, pervaporation and gas permeation test. It is found that small amounts of sodium ions can result in denser and more hydrophobic membranes with higher pervaporation performance. Large amounts of sodium ions will retard the nucleation and bring about the formation of gel particles, hence resulting in lower pervaporation performance. For separation of 5 wt% ethanol feed at 60 degrees C, the separation factor of 76 is achieved at the Na+/Si ratio of 0.1, while it is only 52 without sodium ions in the synthesis solution.