Zeolites are widely used in catalysis, gas separation, ion exchange, etc. due to their superior physicochemical properties, which are closely related to specific features of their framework structures. Although more than two hundred different framework types have been recognized, it is of great interest to explore from a crystallographic perspective, the atomic positions, surface terminations, pore connectivity and structural defects that deviate from the ideal framework structures, namely local structural modulation. In this article, we review different types of local modulations in zeolite frameworks using various techniques, especially electron microscopy (EM). The most recent advances in resolving structural information at the atomic level with aberration corrected EM are also presented, commencing a new era of gaining atomic structural information, not only for all tetrahedral atoms including point vacancies in framework but also for extra‐framework cations and surface terminations.