Transport phenomena play an essential role in catalysis. While zeolite catalysis is widely applied in industrial chemical processes, its efficiency is often limited by the transport rate in the micropores of the zeolite. Experimental and theoretical methods are useful for understanding the transport phenomena on multiscale levels. Traditional diffusion models usually use a linear driving force and an isotropic continuum medium, such that transport in a hierarchical catalyst structure and the occurrence of nonlinear deactivation cannot be well understood. Due to the presence of spatial confinement and an ordered structure, some aspects of the transport in a zeolite cannot be regarded as continuum phenomena and discrete models are being developed to explain these. Graph theory and small-world networks are powerful tools that have allowed pseudo-phase transition phenomena and other nontrivial relationships to be clearly revealed. Discrete models that include graph theory can build a bridge between microscopic quantum physics and macroscopic catalyst engineering in both the space and time scales. For a fuller understanding of transport phenomena in diverse fields, several theoretical methods need to be combined for a comprehensive multiscale analysis.