Microporous framework membranes such as metal-organic framework (MOF) membranes and covalent organic framework (COF) membranes are constructed by the controlled growth of small building blocks with large porosity and permanent well-defined micropore structures, which can overcome the ubiquitous tradeoff between membrane permeability and selectivity; they hold great promise for the enormous challenging separations in energy and environment fields. Therefore, microporous framework membranes are endowed with great expectations as next-generation membranes, and have evolved into a booming research field. Numerous novel membrane materials, versatile manipulation strategies of membrane structures, and fascinating applications have erupted in the last five years. First, this review summarizes and categorizes the microporous framework membranes with pore sizes lower than 2 nm based on their chemistry: inorganic microporous framework membranes, organic-inorganic microporous framework membranes, and organic microporous framework membranes, where the chemistry, fabrications, and differences among these membranes have been highlighted. Special attention is paid to the membrane structures and their corresponding modifications, including pore architecture, intercrystalline grain boundary, as well as their diverse control strategies. Then, the separation mechanisms of membranes are covered, such as diffusion-selectivity separation, adsorption-selectivity separation, and synergetic adsorption-diffusion-selectivity separation. Meanwhile, intricate membrane design to realize synergistic separation and some emerging mechanisms are highlighted. Finally, the applications of microporous framework membranes for precise gas separation, liquid molecule separation, and ion sieving are summarized. The remaining challenges and future perspectives in this field are discussed. This timely review may provide genuine guidance on the manipulation of membrane structures and inspire creative designs of novel membranes, promoting the sustainable development and steadily increasing prosperity of this field.