Metal–organic framework‐based materials are promising single‐site catalysts for electrocatalytic nitrate (NO3−) reduction to value‐added ammonia (NH3) on account of well‐defined structures and functional tunability but still lack a molecular‐level understanding for designing the high‐efficient catalysts. Here, we proposed a molecular engineering strategy to enhance electrochemical NO3−‐to‐NH3 conversion by introducing the carbonyl groups into 1,2,4,5‐tetraaminobenzene (BTA) based metal‐organic polymer to precisely modulate the electronic state of metal centers. Due to the electron‐withdrawing properties of the carbonyl group, metal centers can be converted to an electron‐deficient state, fascinating the NO3− adsorption and promoting continuous hydrogenation reactions to produce NH3. Compared to CuBTA with a low NO3−‐to‐NH3 conversion efficiency of 85.1 %, quinone group functionalization endows the resulting copper tetraminobenzoquinone (CuTABQ) distinguished performance with a much higher NH3 FE of 97.7 %. This molecular engineering strategy is also universal, as verified by the improved NO3−‐to‐NH3 conversion performance on different metal centers, including Co and Ni. Furthermore, the assembled rechargeable Zn−NO3− battery based on CuTABQ cathode can deliver a high power density of 12.3 mW cm−2. This work provides advanced insights into the rational design of metal complex catalysts through the molecular‐level regulation for NO3− electroreduction to value‐added NH3.