Emerging covalent organic frameworks (COFs) have received great attention for their unique features, but the limited building blocks restrict their structural diversity and performance exploration. Reticular chemistry provides guidance for the structural expansion and performance regulation of COFs. Herein, we constructed two novel two‐dimensional (2D) COFs functionalized with cyclopentadienyl cobalt, denoted as UPC‐COF‐1 and UPC‐COF‐2, via [4+2] imine condensation with diamine building blocks of different length. Theoretical simulations combined with experimental results reveal that UPC‐COF‐1 with shorter building blocks, narrower pore sizes, and stronger host‐guest interactions has better C2H2/CO2 separation performance. In addition, UPC‐COF‐1 can maintain separation stability in the presence of water vapor and methane impurities. This work provides a new evidence for the performance regulation of isoreticular COFs with modular and tunable building blocks.