Tropical instability waves (TIWs) play an important role in modulating the physical variability (e.g., sea surface temperature [SST] and heat flux) and biological activity (e.g., phytoplankton and chlorophyll (Chl)) in the eastern tropical Pacific. The impacts of TIW‐induced Chl perturbations (ChlTIW) are examined using a coupled ocean physics‐biology model in the tropical Pacific. TIW‐scale biological and physical perturbations are extracted using a zonal high‐passed filter. The TIW‐induced perturbations of biological and physical fields (e.g., Chl, nitrate, iron, and SST.) exhibit their close relationships, with negative correlation between SST and Chl at TIW scale. Processes responsible for the impacts of ChlTIW are diagnosed. ChlTIW acts to modulate the incoming solar radiation that penetrates the bottom of the mixed layer (Qpen). In addition, two experiments are conducted with the impacts of ChlTIW on the ocean included or not. The results show that the ChlTIW effects tend to substantially increase seasonal variability of eddy kinetic energy (EKE) and slightly decrease SST in the eastern equatorial Pacific. At large scale, ChlTIW leads to an increase in mean Chl concentration, which induces a SST cooling and an increase in EKE in the boreal winter. At TIW scale, ChlTIW leads to the change in Qpen and a decrease in baroclinic conversion term and eventually decreases the EKE in the boreal spring and summer. So the ChlTIW acts to have influences both on the intensity of TIW and large‐scale SST in the tropical Pacific, involving multiscale interactions and feedbacks between ocean physics and biology.