We applied a fluorescence microscopy method to investigate the intercrystalline migration of aromatic molecules adsorbed in faujasite zeolites aiming at observing directly the particle-to-particle processes dependent both on interparticle distance and on the time scale of the observation. Photophysical processes such as intersystem crossing and energy transfer and photochemical reactions such as charge transfer (CT) and triplet-triplet energy transfer between guest species incorporated in the zeolites were exploited as indicator reactions to yield a luminescence color characteristic of individual zeolite particles. Two types of migration mechanisms were observed: a through-space diffusional transfer mode between separated zeolite crystals and a molecular injection process from a loaded crystal to another unloaded crystal, both in contact. A preferential direction of guest migration was found to exist for a few cases: for instance, aromatics such as phenanthrene and chrysene migrate from sodium form of zeolite X (Na+-X) to thallium-exchanged zeolite X (Tl+-X). On the other hand, the migration-assisted formation of CT complexes between electron-donating arenes such as phenanthrene and chrysene, and electron-accepting 1,2,4,5-tetracyanobenzene, both incorporated into separate zeolite Na+-X crystals, takes place as a result of the migration of the donors. Comparison of this technique with a conventional fluorescence spectroscopic method for zeolite powders revealed that the microscopy method is advantageous because it is difficult for the spectroscopic method to detect the evolution of new emission bands in strongly emitting matrix. The fluorescence microscopy method utilizing photochemistry in zeolites was found to be a powerful technique for the qualitative investigation of the intercrystalline migration in zeolites.