Tropical instability waves (TIWs) induce large physical and biological perturbations, which have a feedback onto the tropical Pacific climate and ecosystem. However, the extent to which TIW‐induced chlorophyll perturbations (ChlTIW) can influence El Niño–Southern Oscillation (ENSO) remains unknown. Here we used a hybrid‐coupled model to investigate the ChlTIW effect on ENSO. Two experiments are conducted, one with the ChlTIW effect being represented in the control run (CTRL) and other with the ChlTIW effect being purposely excluded by filtering out ChlTIW signals (FILT). Results show that the amplitude of ENSO is increased by 27% in CTRL compared to FILT. ChlTIW tends to modulate the penetrative solar radiation in the upper ocean, acting to weaken the intensity of TIWs. Then, the weakened TIWs lead to a reduction in the equatorward meridional heat transport and consequently less warming effect on the cold tongue. Therefore, La Niña conditions tend to be intensified, and ENSO amplitude is increased.