Nanoporous materials contains a methodical organic or inorganic framework supporting a regular , porous structure. The size of the pores is generally 100 nm or smaller. Most nanoporous materials are often classified as bulk materials or membranes. The nanoporous catalysts with advantages of high surface areas and abundant nanoporosity have been widely used in heterogeneous catalytic processes, but their catalytic performances are generally lower than those of the corresponding homogeneous catalysts due to distinguishable exposed active sites and molecular diffusion. Recent results show that molecular diffusion strongly influences catalytic performances. Therefore, adjusting the molecular diffusion in the nanoporous catalysts is an efficient route for catalytic enhancement of heterogeneous catalysts. In this chapter, recent developments are briefly summarized on rational adjustment of molecular diffusion in the heterogeneous nanoporous catalysts, including the use of hierarchical zeolites for fast mass transfer, active sites such as metal and metal oxide nanoparticles fixed inside nanoporous crystals such as zeolites and MOFs for shape-selective diffusion, and employment of nanoporous polymer-based catalysts for controlling the catalyst wettability, where the relationship between molecular diffusion and catalytic properties is particularly emphasized. Finally, the perspectives and challenges for the adjustment of molecular diffusion in the heterogeneous catalysts such as sustainable preparation of hierarchical zeolites and introduction of functionalized groups in the nanoporous catalysts are discussed.