Crystalline porous materials (CPMs) with large surface areas, adjustable pore sizes, and tunable chemical properties show great potential in pollutant removal. Rational design of the microenvironments and configurations of CPMs can ameliorate adsorption. Here we introduce vacancies and adsorption sites into CPMs by defect construction for enhancing iodine capture performance. Through simple monocarboxylic acid regulation, the prepared metal–organic frameworks (MOFs), a class of CPMs, exhibit massive cluster-missing defects and functionalized terminals with contents over 28.2%. Because of the improved chemical properties of metal centers, phenyl sites, and terminal COOH groups and the superior structure characteristics of porosities and pore sizes, the MOFs show impressive iodine capture, with 2–50 times of adsorption rate and 2–5 times of capacity than most conventional MOFs, accompanied by commendable reusability. This superb performance reveals that designing defects is an efficient strategy for microstructural engineering of CPMs with great potential in adsorption and storage for chemical, environmental, and energy-related applications.