Chlorophyll in phytoplankton modulates upper-ocean heating by absorbing shortwave radiation, thereby affecting climate systems. However, how chlorophyll influences multi-year La Niña evolution—a key aspect of El Niño–Southern Oscillation diversity—remains largely unexplored. Using a coupled ocean physics–biogeochemical model, we reveal that chlorophyll patterns markedly modulate the anomalous zonal sea surface temperature gradient across the equatorial Pacific. In the western-central equatorial Pacific, increased surface chlorophyll enhances meridional advection and vertical mixing, sustaining cooling into the second year by ~8%. Conversely, reduced chlorophyll in the eastern equatorial Pacific allows deeper shortwave penetration, warming the subsurface; this subsequently promotes surface warming by ~45% via background upwelling. Additionally, the subsurface chlorophyll maximum further enhances eastern equatorial Pacific cooling, helping sustain second-year La Niña conditions. These findings identify phytoplankton-driven bio-feedback as a previously unrecognized mechanism reshaping multi-year La Niña processes.