Separation of xylene isomers by MFI zeolite membrane and using of pervaporation process are of interested researchers. The isomorphous substitution of trivalent boron in MFI zeolite structure by applying a novel microwave-assisted “two-stage varying temperature” hydrothermal synthesis method was investigated in this study. The effects of template concentration in the sol composition, aging/stirring time, Si/B ratio and second stage time and temperature on the size, morphology and zeolite formation yield were of interest. At the first stage, nucleation and maturation of zeolite precursors was carried out at 80°C for 90 min, whereas, the crystallization was done during the second stage at temperature range of 120-175°C and crystallization time in the range of 30-60 min. Si/B ratio after synthesis was recorded by ICP-AES test. Crystallites size and powder recovery varied from 75 to 410nm and from 26.9 to 100 (%w/w), respectively for 120 and 175°C. Also, crystallinity of MFI phase reached 100% after 60min crystallization at 140°C. To synthesis of zeolite membranes, the B-MFI powder with high crystallinity and lowest second step temperature was used. For this purpose, firstly alumina support seeded with B-MFI powder by dip coating method. Calcination was done by exact temperature rate control to remove organic template from zeolite structure. The coated support, then transferred to the teflon-autoclave and filled by template-free solution. In this step, effects of zeolite powder concentration in suspension, microwave synthesis temperature and seeding time on membranes were investigated. Growth of seeds were done by subjecting of support and solution with microwave heating at 175°C during 40-60 min. The resulted membranes had a 3-3.6 micrometer thickness. . Synthetic membranes were evaluated for separation of p-xylene from o-xylene with pervaporation process. Effects of p-xylene concentration in feed stream and process temperature on p-xylene flux and selectivity were investigated. The results shown that the best value for selectivity was 360 at feed temperature of 25°C and 5% p-xylene concentration in feed. These results were yielded for membrane that synthesized in 1.5% zeolite powder suspension, 60 min seeding time and 60 min microwave heating conditions. Also, stability of membranes for 24h process showed that this membrane had a good stability because of application new synthetic methods in membranes syhnthesis. In sum, utilization of microwave heating, nano-size zeolite powder, template-free solution and incorporation of boron in MFI zeolite membrane lowered costs, decreased synthesis time and refined membrane yield in xylene isomers separation.