The persistent paradox in electrochemical nitrate reduction (NO3-RR)─the requirement of high overpotentials despite its highly exothermic nature─remains a critical roadblock for efficient ammonia electrosynthesis. Here, we resolve this conundrum by identifying a high-valent anionic intermediate as kinetic gatekeepers during the nitrate reduction on a single-atom catalyst by using AIMD simulations under explicit solvation and electrode potentials. Employing our self-developed constant-potential thermodynamic integration method, we reveal a stark kinetic barrier dichotomy: while the reaction is thermodynamically favorable governed by the N-O break, the protonation to oxygen at a low anionic state necessitates substantial activation energy. Mechanistic analysis uncovers that electrode polarization preactivates *NO3- into a metastable high-valent *NO32- intermediate, which serves as the key step to the following protonation process. Crucially, this intermediate's stabilization requires a highly negative potential, directly linking its formation to the observed overpotential. Furthermore, molecular dynamics simulations also demonstrate that K+ cations play a key role in electrostatically stabilizing the adsorption of negatively charged NO3- onto the negatively polarized cathode. This work calls for the urgent reconsideration of conventional nitrate reduction mechanisms and the exigency of refined interface design principles for improved nitrate electrocatalysis.