Oceanic fine-scale processes, encompassing mesoscale and submesoscale eddies, are highly active in the equatorial Pacific, regulating the tropical climate by modulating heat transport. However, their response to greenhouse warming remains largely unconstrained. Here, using high-resolution climate projections, we reveal a scale-dependent divergent response of equatorial eddies to anthropogenic warming. Specifically, mesoscale tropical instability waves intensify whereas submesoscale eddies undergo a widespread decay. Mesoscale intensification is driven by reorganized equatorial currents enhancing barotropic energy conversion alongside attenuated wind-current feedback reducing dissipation. Conversely, submesoscale suppression stems from reduced baroclinic energy conversion. This reduction is governed by an El Niño-like warming pattern that intensifies upper-ocean stratification and weakens the cold tongue front. Despite increased mesoscale kinetic energy, horizontal eddy heat flux diminishes as inhomogeneous warming flattens the meridional temperature gradient. Concurrently, submesoscale suppression severely restricts vertical heat flux. Thus, our study suggests a complex change in tropical fine-scale processes under greenhouse warming, potentially reshaping regional climate and marine ecosystems.