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Bipolar membranes (BPMs) have emerged as a promising solution for mitigating CO2 losses, salt precipitation and high maintenance costs associated with the commonly used anion‐exchange membrane electrode assembly for CO2 reduction reaction (CO2RR). However, the industrial implementation of BPM‐based zero‐gap electrolyzer is hampered by the poor CO2RR performance, largely attributed to the local acidic environment. Here, we report a backbone engineering strategy to improve the CO2RR performance of molecular catalysts in BPM‐based zero‐gap electrolyzers by covalently grafting cobalt tetraaminophthalocyanine onto a positively charged polyfluorene backbone (PF‐CoTAPc). PF‐CoTAPc shows a high acid tolerance in BPM electrode assembly (BPMEA), achieving a high FE of 82.6 % for CO at 100 mA/cm2 and a high CO2 utilization efficiency of 87.8 %. Notably, the CO2RR selectivity, carbon utilization efficiency and long‐term stability of PF‐CoTAPc in BPMEA outperform reported BPM systems. We attribute the enhancement to the stable cationic shield in the double layer and suppression of proton migration, ultimately inhibiting the undesired hydrogen evolution and improving the CO2RR selectivity. Techno‐economic analysis shows the least energy consumption (957 kJ/mol) for the PF‐CoTAPc catalyst in BPMEA. Our findings provide a viable strategy for designing efficient CO2RR catalysts in acidic environments. [ABSTRACT FROM AUTHOR]