Metal-organic frameworks (MOFs) have been widely employed in gas storage and separation, drug delivery, and catalysis. The design and construction of MOFs and their hierarchical assemblies play a key role in enhancing properties including guest diffusion kinetics, catalytic activity, and selectivity. This Review summarizes the most recent advances in the controlled synthesis of MOFs with tunable sizes and morphologies, discusses the programmed assembly of novel MOFs with hierarchical structures, and highlights the vital roles of composition, morphology, and the hierarchically porous structure in applications, including delivery and catalysis. A short review of programmable assembly of MOF superstructures and composites with hierarchically arranged functionalities is provided. Taken together, this Review is expected to supply synthetic guidance for developing MOFs and their hierarchical assemblies, which shall in turn guide the state-of-the-art design of sophisticated materials with unprecedented tunability for various applications.