Mesoscale eddies are known to substantially modulate vertical exchanges of oceanic heat, salt, and nutrients, yet the dynamical processes underlying such exchanges and their impacts on vertical velocities remain poorly understood. Classical vertical-velocity diagnostic methods build upon density equation only consider self-evolution of mesoscale eddies while neglecting effects from large-scale background field. Here, we establish a comprehensive vertical-velocity diagnostic framework, which includes traditional tendency and self-advection terms of mesoscale eddies, alongside two eddy-flow interaction terms: advection of mesoscale density anomalies by large-scale flow and advection of large-scale density by mesoscale currents. Using GLORYS reanalysis and mooring observations, we quantify these terms in the Kuroshio Extension and find that the vertical velocity amplitudes induced by eddy-flow interactions are comparable to those arising from eddy tendency and self-advection. The diagnosed vertical velocities can reach magnitudes of O(100) m day⁻¹, resulting in significant vertical heat transport. These findings highlight that eddy-flow interactions exert critical controls on mesoscale‑associated vertical velocities and advance our understanding of ocean mesoscale dynamics.