Phytoplankton biomass substantially influences the Arctic climate via biogeophysical feedback, i.e., an increase in the mean chlorophyll concentration absorbs more shortwave radiation in the surface ocean layer, which leads to Arctic surface warming. Here, we identified that in addition to the effect of the mean chlorophyll change, an interannual chlorophyll variability substantially influences the Arctic mean climate state, even though the mean chlorophyll remains the same. We found that two nonlinear rectifications of chlorophyll variability induced Arctic cooling. One was due to the effect of a nonlinear shortwave heating term, which was induced by the positive ice–phytoplankton covariability in the boreal summer. The other was due to a cooling effect by rectification of a nonlinear function of the shortwave absorption rate, which reduced the shortwave absorption rate by interannually varying chlorophyll. In the Coupled Model Intercomparison Project, earth system models that included biogeophysical feedback simulated a colder Arctic condition than models without a biogeophysical feedback. This result suggests a possible mechanism in understanding how chlorophyll variability interacts with the Arctic climate system and its impact on the Arctic mean climate state.