Optimizing the coordination structure and microscopic reaction environment of isolated metal sites is promising for boosting catalytic activity for electrocatalytic CO2 reduction reaction (CO2RR) but is still challenging to achieve. Herein, a newly electrostatic induced self‐assembly strategy for encapsulating isolated Ni‐C3N1 moiety into hollow nano‐reactor as I‐Ni SA/NHCRs is developed, which achieves FECO of 94.91% at −0.80 V, the CO partial current density of ≈−15.35 mA cm−2, superior to that with outer Ni‐C2N2 moiety (94.47%, ≈−12.06 mA cm−2), or without hollow structure (92.30%, ≈−5.39 mA cm−2), and high FECO of ≈98.41% at 100 mA cm−2 in flow cell. COMSOL multiphysics finite‐element method and density functional theory (DFT) calculation illustrate that the excellent activity for I‐Ni SA/NHCRs should be attributed to the structure‐enhanced kinetics process caused by its hollow nano‐reactor structure and unique Ni‐C3N1 moiety, which can enrich electron on Ni sites and positively shift d‐band center to the Fermi level to accelerate the adsorption and activation of CO2 molecule and *COOH formation. Meanwhile, this strategy also successfully steers the design of encapsulating isolated iron and cobalt sites into nano‐reactor, while I‐Ni SA/NHCRs‐based zinc‐CO2 battery assembled with a peak power density of 2.54 mW cm−−2 is achieved.