Highly permselective and durable membrane materials have been sought for energy-efficient C3H6/C3H8 separation. Mixed-matrix membranes (MMMs) comprising a polymer matrix and metal–organic frameworks (MOFs) are promising candidates for this application; however, rational matching of filler-matrix is challenging and their separation performances need to be further improved. Here, we propose a novel strategy of “defect engineering” in MOFs as an additional degree of freedom to design advanced MMMs. MMMs incorporated with defect-engineered MOFs exhibit exceptionally high C3H6 permeability and maintained C3H6/C3H8 selectivity, especially with enhanced stability under industrial mixed-gas conditions. The gas transport, sorption, and material characterizations reveal that the defect sites in MOFs provide the resulting MMMs with not only ultrafast diffusion pathways but also favorable C3H6 sorption by forming complexation with unsaturated open metal sites, confirmed by in situ FT-IR studies. Most importantly, the concept is also valid for different polymer matrices and gas pairs, demonstrating its versatile potential in other fields.