The advent of two-dimensional nanomaterials, a revolutionary class of materials, is marked by their atomic-scale thickness, superior aspect ratios, robust mechanical attributes, and exceptional chemical stability. These materials, producible on a large scale, are emerging as the forefront candidates in the domain of membrane-based gas separation. The concept of defect engineering in 2D nanomaterials has introduced a novel approach in their application for membrane separation, offering an effective technique to augment the performance of these membranes. Nonetheless, the development of customized microstructures in gas separation membranes via defect engineering remains nascent. Hence, this review is designed to serve as a comprehensive guide for the application of defect engineering in 2D nanomaterial-based membranes. It delves into the most recent developments in this field, encompassing the synthesis methodologies of defective 2D nanomaterials and the mechanisms underlying gas transport. Special emphasis is placed on the utilization of defect-engineered 2D nanomaterial-based membranes in gas capture applications. Furthermore, the paper encapsulates the burgeoning challenges and prospective advancements in this area. In essence, defect engineering emerges as a promising avenue for enhancing the efficacy of 2D nanomaterial-based membranes in gas separation, offering significant potential for advancements in membrane-based gas separation technologies.