Recent studies show that climate change signals in the long‐term trend of the tropical ecosystems have emerged earlier than projected by climate models. However, it remains unclear whether tropical ocean surface chlorophyll (SChl) shows a robust trend in the available satellite data era, and what possible physical mechanisms can be responsible for this trend. Here, using combined data from observations, hindcast biogeochemical simulations, and climate model outputs, we document consistently decreasing trends of SChl in the three ocean basins (Indian Ocean, Pacific Ocean, and Atlantic Ocean) with varying magnitude from −1.6% to −10.0% per decade during 1998–2020, with tropical ocean SChl showing a decreasing trend of −7.1% per decade. In the Indo‐Pacific Ocean, mechanisms for the two hotspots with significantly decreasing SChl trends are identified. (a) In the northern tropical Pacific, under the anthropogenic forcing, enhanced stratification associated with frequent interannual surface warming overwhelms the Ekman pumping effect due to positive wind stress curl, leading to a decrease in SChl. (b) In the southern tropical Indian Ocean, the downwelling process dominates the decreasing SChl trend due to the Ekman pumping associated with the negative wind stress curl prevailing in the Indian Ocean, while the contribution from the stratification change is negligible. This study identifies two hotspots with consistently decreasing SChl trends in the tropical ocean which are influenced by the complex physical processes under a warmer climate and calls for more comprehensive understanding of the interactions between physical processes and biogeochemical cycles in the tropical ocean ecosystems.