MFI-type zeolites have a medium pore size of 0.56nm. Defect-free MFI zeolite membranes (i.e. single crystal) can be used for separation of xylene isomers with high selectivity toward p-xylene (PX) primarily based on molecular sieving effect. However, the inherent nanoscale intercrystalline pores in the polycrystalline MFI zeolite membranes can cause serious decline in the PX separation factor. Although the nonselective intercrystal pores were known to be one of the major factors responsible for the lower-than-expected selectivity in zeolite membrane separations, quantitative evaluations of the effect of intercrystal pores on the separation performance has been so far very limited. In this work, we developed a mathematic model to quantitatively analyze the xylene fluxes through the nonselective intercrystal pores during permeation of xylene vapor mixtures and estimate the decreases in xylene permselectivity and separation factors caused by such leaking through the intercrystal pores. The theoretical analysis is based on the experimental data of xylene single component permeation and vapor mixture separation. Tubular MFI-type zeolite membranes synthesized by in-situ crystallization from an Al-free precursor were used in the experimental work. A new method of online membrane modification by carbonization of 1,3,5-triisopropylbenzene in the feed stream was developed and found to be effective for reducing the intercrystalline pores and improving the PX separation.