Single-atom catalyst has garnered widespread attention to mimic mature enzymes due to its well-defined atomic structure and coordination environments. However, since the carbon-carbon (C–C) coupling reactions require synergistic catalysis of multiple sites, single-atom catalysts suffer from insufficient active sites and unclear reaction mechanisms. Controlling the reaction intermediates in a precisely targeted pocket through careful metal-organic cage design is therefore crucial. Here, we prepare a tetrahedral [Cu6L4]-type boron–imidazolate cage integrating highly active Cu sites and optimized cavity, which exhibits enzyme like specific catalytic performance in electrochemical CO2 reduction reaction (CO2RR) to enhance the selectivity of C2H4. Electrochemical analyses and computational calculations suggest that the single Cu site together with neighboring boron-imidazolate ligands provides suitably synergistic effects that enable the energetically favorable formation of an *COCHO intermediate, a key step determining selectivity. As a result, the [Cu6L4]-type cage of BIC-145 achieves a Faradaic efficiency of 28% for C2H4 maintaining an average current density of −3.54 mA cm−2 over a 5-hour electrolysis period. This work represents the first example for studying single-metal site catalysts with ultra-low coordination numbers through the rational design of metal-organic cages.