Pacific warming is accelerating ocean deoxygenation and threatening phytoplankton diversity. However, detecting warming-induced phytoplankton and oxygen trends and phytoplankton adaptive responses to warming remain largely unexplored, particularly over long-term observations. Herein, we establish a Bayesian-mechanistic model and incorporate a unique light-driven phytoplankton migration mechanism to assess the countervailing effects of Pacific warming on phytoplankton and oxygen dynamics and associated rigorous uncertainties. The present study indicated a considerable overestimation of phytoplankton light exposure under commonly applied light attenuation estimation by ignoring phytoplankton-light feedback. Subtropical phytoplankton presented weak migratory potential to ambient irradiance, while tropical taxa have engaged in dive migration strategy to mitigate photoinhibitory-induced declines in production. Moreover, physical mixing, rather than thermally-driven changes in oxygen solubility, predominantly drives Pacific deoxygenation. Such an analysis would permit the complete evaluation of the complex interplay between climate change and marine ecosystems.