Controversy has surrounded the potential impacts of phytoplankton on the tropical climate, since climate models produce diverse behaviors in terms of the equatorial mean state and El Niño-Southern Oscillation (ENSO) amplitude. We explored biophysical impacts on the tropical ocean temperature using an ocean general circulation model coupled to a biogeochemistry model in which chlorophyll can modify solar attenuation and in turn feed back to ocean physics. Compared with a control model run excluding biophysical processes, our model with biogeochemistry showed that subsurface chlorophyll concentrations led to an increase in sea surface temperature (particularly in the western Pacific) via horizontal accumulation of heat contents. In the central Pacific, however, a mild cold anomaly appeared, accompanying the strengthened westward currents. The magnitude and skewness of ENSO were also modulated by biophysical feedbacks resulting from the chlorophyll affecting El Niño and La Niña in an asymmetric way. That is, El Niño conditions were intensified by the higher contribution of the second baroclinic mode to sea surface temperature anomalies, whereas La Niña conditions were slightly weakened by the absorption of shortwave radiation by phytoplankton. In our model experiments, the intensification of El Niño was more dominant than the dampening of La Niña, resulting in the amplification of ENSO and higher skewness.