Mixed matrix membranes (MMMs), which are fabricated by incorporating dispersed fillers into a continuous polymeric matrix, have been broadly utilized in gas separation due to their unique hierarchical structures and enhanced separation performance. Fillers of intrinsic nanopores (FINs) have drawn considerable attention because they not only can provide additional molecular transport channels but also have a potential size-sieving property. Although many excellent reviews about MMMs have been published, quite few of them are specifically designed for MMMs containing FINs. This Review focuses on three kinds of FINs, covalent organic frameworks (COFs), zeolites, and metal-organic frameworks (MOFs), as the representatives of organic, inorganic, and inorganic-organic FINs. The typical physical and chemical features of these three kinds of FINs are introduced. Afterward, methods to prepare FIN-based MMMs are briefly introduced. Particularly, solutions to prevent the aggregation and improve the dispersion of FINs within the polymeric matrix are proposed. Next, this Review will discuss the applications of FIN-based MMMs in gas separation including carbon dioxide capture and alkanes/olefins separation. Finally, the tentative perspective on the research and development of FIN-based MMMs will be presented.