Abstract Unveiling structure-activity correlations at the sub-nanoscale remains an essential challenge in catalysis science. During electrocatalysis, dynamic structural evolution drives the ambiguous entanglement of crystals and electrons degrees of freedom that obscure the activity origin. Here, we track the structural evolution of Ni-based model pre-catalysts (Ni(OH)2, NiS2, NiSe2, NiTe), detailing their catalytically active state during water oxidation via operando techniques and theoretical calculations. We reveal the sub-nanometric structural difference of NiO6 unit with a regular distortion in the reconstructed active phase NiOOH, codetermined by the geometric (bond lengths) and electronic (covalency) structure of the pre-catalysts on both spatial and temporal scales. The symmetry-broken active units induce the delicate balance of the p and d orbitals in NiOOH, further steering the modulation of catalytic intermediate configurations and mechanisms, with improved performance. This work recognizes the fine structural differences of the active phases from the sub-nanometer scale, and quantitatively explains their influence on activity. Our findings provide a more intuitive design framework for high-efficiency materials through targeted symmetry engineering of active units.