This paper reviews diverse capabilities offered by modern electron microscopy techniques in studying fine structures of nanoporous crystals such as zeolites, silica mesoporous crystals, metal organic frameworks and yolk-shell materials. For the case of silica mesoporous crystals, new approaches that have been developed recently to determine the three-dimensionally periodic average structure, e.g., through self-consistent analysis of electron microscope images or through consideration of accidental extinctions, are presented. Various structural deviations in nanoporous materials from their average structures including intergrowth, surface termination, incommensurate modulation, quasicrystal and defects are demonstrated. Ibidem observations of the scanning electron microscope and atomic force microscope give information about the zeolite-crystal-growth mechanism, and an energy for unstitching a building-unit from a crystal surface is directly observed by an anatomic force microscope. It is argued how these observations lead to a deeper understanding of the materials.