There is little information about the relationship between aerobic anoxygenic photoheterotrophic bacteria (AAPB) and upwelling. In this work, the response of AAPB to upwelling in the southern Taiwan Strait was examined, using the “Time-series observation-based cyanobacteria-calibrated InfraRed Epifluorescence Microscopy, TIREM”. The results showed that in the initial stage of upwelling, the abundances of AAPB and total heterotrophic bacteria were low; with the development, their abundances both increased and reached the highest value at the mature stage of upwelling; notably, when the upwelling declined, they began to decrease. During the developmental process of upwelling, AAPB abundance was positively correlated with chlorophyll a concentration in a certain range, and limited by low phosphorus concentration, while total heterotrophic bacteria abundance was positively correlated with nitrogen, phosphorus and silicon nutrients concentration, suggesting that dissolved organic carbon released by phytoplankton and phosphorus limitation might play a more direct and important role in AAPB, while nutrients probably acted as an important role in the response of total heterotrophic bacteria to upwelling. This study will help to better understand the unique role of AAPB in the biogeochemical cycle of carbon and other biogenic elements.