A multi-site functionalized microporous metal-organic framework (MOF), H[Zn₂(BDP)_0.5(ATZ)₃]·0.5H₂O·0.5DMF (1), was synthesized through mixed ligands strategy. The pore surface of complex 1 was modified by uncoordinated carboxylate O atoms, phenyl and pyridyl rings as well as -NH₂ groups, which strengthen interactions with C₂H₆, C₂H₄ and CO₂ molecules and lead to efficiently selective C₂H₆, C₂H₄ and CO₂ uptake over CH₄. The selective adsorption mechanism was discussed deeply based on Grand Canonical Monte Carlo (GCMC) simulations. It is expected that this study will provide a new perspective for the rational design and synthesis of MOFs with efficient gas adsorption and separation performance.