[1] Carbon, nitrogen, and chlorophyll are three commonly used variables to quantify phytoplankton productivity. However, owing to the complex effect of light, temperature, and nutrient, these three variables are usually decoupled from each other. By implementing a biogeochemical model that treats phytoplankton carbon, nitrogen, and chlorophyll separately in a Pacific basin-scale circulation model, we have investigated the physical and biogeochemical controls on phytoplankton C:Chl and C:N ratios at different scales. The model reproduces the general features of phytoplankton dynamics in the Pacific basin. Model results indicate a region dependent pattern of driving mechanisms for C:Chl ratio, where C:Chl is largely controlled by light condition in high latitude, by light and nutrient levels in midlatitude, and by nutrient and temperature in the equatorial Pacific, while C:N ratio seems to be region independent and is mostly determined by nutrient and temperature. Pacific basin-scale empirical orthogonal functions (EOF) decompositions suggest both C:Chl and C:N are regulated by the El Niño/Southern Oscillation (ENSO) events to the first-order variability. Owing to the variation of C:Chl, the decoupling between phytoplankton carbon and chlorophyll exists, especially at seasonal and long-term temporal scales. Climate change can affect phytoplankton pigment, biomass, and physiological state. As a consequence, using chlorophyll as a proxy for phytoplankton biomass to interpret decadal variation or long-term trend might be with bias.