The storage flux, corresponding to disequilibrium between observed flux and net surface emissions, poses a significant source of uncertainty in tower-based eddy covariance (EC) measurements over urban and forest ecosystems. In this study, we investigated the coupling between the urban inertial sub-layer (ISL) and roughness sub-layer (RSL) and its influence on nighttime storage flux, leveraging tower-EC together with collocated wind profile measurements. Our findings demonstrate that substantial storage flux occurs when the gradient of turbulent kinetic energy (TKE) enlarges, indicating decoupling between ISL and RSL. With increasing wind speed, turbulent eddies generated by bulk wind shear directly interact with the surface, conducive to the recoupling between ISL and RSL and resulting in decreased storage flux. Conversely, when the gradient of TKE between ISL and RSL is small, the storage flux remains low and relatively insensitive to wind speed. The derived diagnostic relation further confirms the predominant influence of stability and turbulent intensity gradient on regulating the storage flux. These results provide valuable insights as a complement to prior storage flux studies in the context of canopy flow.