Breaking the long-standing permeability–selectivity trade-off remains a central challenge in membrane-based carbon dioxide separations. Here we report a heteroatom-engineering strategy that leverages structurally precise covalent organic frameworks (COFs) to transcend this limitation in mixed matrix membranes (MMMs). Two isostructural, π-conjugated two-dimensional COFs, TUS-621 and TUS-622, were rationally designed through symmetry-guided reticulation of a hexatopic triphenylene node with oxygen- and sulfur-containing diamine linkers, respectively, enabling systematic modulation of pore surface chemistry without altering topology. When incorporated into a Pebax polymer matrix, these COFs function as CO2-philic, molecularly defined transport domains that synergistically couple preferential CO2 sorption with ordered and fast diffusion channels. The optimized TUS-621/Pebax-10% membrane exhibits a CO2 permeability of 433 Barrer with a CO2/CH4 selectivity of 55.3 under mixed-gas conditions, decisively surpassing the 2008 Robeson upper bound for CO2/CH4 separation while simultaneously achieving high CO2/H2 separation performance (CO2 permeability of 407 Barrer and selectivity of 25.2). Comprehensive pressure- and temperature-dependent permeation studies reveal that selectivity remains remarkably stable over 2–10 bar and 25–100 °C, underscoring the robustness of the COF-enabled transport pathways. Long-term operation over 30 days shows negligible performance decay, highlighting excellent resistance to physical aging and interfacial degradation. Comparative analysis establishes that oxygen-rich pore environments in TUS-621 impart stronger CO2 affinity and higher accessible surface area than the sulfur-containing analogue, directly translating molecular-level design into macroscopic separation performance. This work demonstrates that heteroatom-engineered COFs provide a powerful platform for overcoming fundamental transport trade-offs and advancing MMMs toward practical, high-efficiency CO2 separations.