The export flux of particulate organic carbon (POC) is a key parameter for quantifying the capacity of the marine biological pump. However, owing to a lack of observational data, remote sensing‐based studies on global POC export flux remain insufficient, and existing estimates carry considerable uncertainty. In this study, we used a model developed from BGC‐Argo profile data to derive global ocean primary productivity and phytoplankton size structure, which served as critical inputs to a food web model. This approach yielded a global annual mean POC export flux of approximately 9.5 Pg C yr⁻¹ over the past two decades. Comparisons with in situ observations demonstrate that the model‐derived POC export flux is reliable in both magnitude and temporal trend. Further analysis reveals pronounced spatial heterogeneity in both the magnitude and temporal variability of POC export flux. Over the past two decades, the flux has exhibited a significant decreasing trend in the tropical eastern Pacific, while increasing trends are observed in parts of the Southern Ocean and the Indian Ocean. Globally, the annual total POC export flux has shown a fluctuating decline.