A coupled ocean general circulation model (OGCM)‐ocean ecosystem model is used to investigate the effects of the deep chlorophyll maximum (DCM) on the ocean state in the equatorial Pacific Ocean. Climatological and interannual three‐dimensional (3‐D) chlorophyll (CHL) fields are captured well in control runs using the coupled ocean physics‐ecosystem model forced by prescribed atmospheric fields. Further sensitivity experiments are performed to assess the effects of 3‐D CHL structure using the OGCM with the prescribed CHL fields taken from the control runs: CHLclim and normalCnormalHnormalLnormalcnormallnormalinormalmnormalsnormalunormalrnormalf ${\mathrm{C}\mathrm{H}\mathrm{L}}_{\mathrm{c}\mathrm{l}\mathrm{i}\mathrm{m}}^{\mathrm{s}\mathrm{u}\mathrm{r}\mathrm{f}}$ are runs in which climatological DCM effect is included or only surface CHL effect is included; CHLinter and normalCnormalHnormalLnormalinormalnnormaltnormalenormalrnormalsnormalunormalrnormalf ${\mathrm{C}\mathrm{H}\mathrm{L}}_{\mathrm{i}\mathrm{n}\mathrm{t}\mathrm{e}\mathrm{r}}^{\mathrm{s}\mathrm{u}\mathrm{r}\mathrm{f}}$ are runs with interannually varying DCM effects included or not. The differences in the simulated ocean conditions are analyzed to explore DCM effects on sea surface temperature (SST) and amplitude of El Niño‐Southern Oscillation (ENSO). Two competing mechanisms responsible for the DCM effects are revealed: an ocean biology‐induced direct heating (OBH) effect, and an indirect cooling effect due to dynamic processes associated with vertical mixing and shallow meridional overturning circulation. There are three major findings: (a) DCM acts to reduce mean SST by around 0.2°C in the eastern equatorial Pacific, being larger than the surface CHL effects. (b) DCM interannual variability increases the ENSO amplitude to a comparable degree as the surface CHL effects. (c) The total net impact of vertical mixing, currents, and net surface heat flux makes SST drop more under the DCM effect than the surface CHL effect in the eastern Pacific. These findings provide a new insight into the feedback mechanisms for the bioclimate interactions.