The capture of sulfur hexafluoride (SF6) and carbon dioxide (CO2) is an important but challenging task for reducing greenhouse gas emission and thereby diminishing negative impacts of global climate change. Herein, we integrated local nanomolecular traps into an inexpensive cobalt-based metal–organic framework (MOF, namely GNU-3) with suitable pore sizes and functional pore surfaces for capturing greenhouse gases. Activated GNU-3a showed good adsorption and separation properties for SF6 and CO2. Especially for SF6, GNU-3a displayed the high SF6/N2 (10:90, v/v) selectivity of 317.6 and SF6 uptake capacity of 2.63mmol/g at 298 K and 1.0 bar. Grand canonical Monte Carlo simulations and first-principles dispersion-corrected density functional theory calculations identified that gas molecules were favorably trapped in polyaromatic ring functionalized channel centers and nanomolecular traps of pore walls by the strong hydrogen bond interactions. Excellent breakthrough results recommend practical separating properties of GNU-3a for binary SF6/N2 and CO2/N2 mixtures, and ternary SF6/CO2/N2 mixtures. Moreover, benefitting from superior features of cheap raw materials and large-scale synthesis, GNU-3 is expected to be applied to practical industrial scenarios. This work may provide insights into constructing prospectively industrial porous MOF adsorbents with optimal pore structures for greenhouse gas capture.