The applications of nanoporous crystalline materials are closely related to the mass transfer of guest molecules. However, the fundamental knowledge of mass transfer, and in particular the surface barriers controlled by the permeation of guest molecules through the external surfaces of materials, is still incomplete. The diversity of surface permeability at the single-crystal level, caused by the varying origins of surface transport resistance, hinders the rational materials design and needs better understanding. Herein, we probe the molecular transport in single zeolite crystals with fluorescent 4-(4-diethylaminostyryl-1-methylpyridinium iodide) (DAMPI) using super-resolution structured illumination microscopy (SIM). It showed that both the inter- and intra-crystal diversity of surface barriers could be monitored by detecting the diffusion behaviors on the center and surface planes in single crystals. This adds a new perspective for studying the origins of the surface barriers as well as the molecular transport mechanisms in nanoporous materials.