This study aimed to comprehend the effects of Typhoon Maria on the pelagic ecosystem in the southern East China Sea. Shipboard measurements were conducted at eight sampling stations before (2–4 d) and after (3–6 d) the typhoon, which enabled the evaluation of the potential impacts of the typhoon on this pelagic ecosystem, with particular focus on carbon dynamics. Following the typhoon's passage, there was a slight drop in sea surface temperature. The response of the variables to the typhoon, however, exhibited variations at different sampling stations. For further analysis, t‐tests compared variables, while type II regression assessed the linear correlation between two variables. Overall, during the post‐typhoon period, concentrations of nitrate, chlorophyll a, primary production, bacterial biomass and production, plankton community respiration, and abundance of large phytoplankton (> 2 μm) and the relative abundance of picophytoplankton among larger‐sized picoeukaryotes were higher compared to the pre‐typhoon period. The mean value of fugacity of CO2 was similar to or slightly lower than pre‐typhoon period. Although the typhoon‐induced vigorous primary production might have absorbed a significant amount of CO2, the decrease in fugacity of CO2 could have been offset by the plankton community respiration. The findings suggest that the typhoon enhanced physical disturbance and increased water column mixing, which, in turn, augmented nutrient availability and promoted plankton growth in the shallow water column. Overall, this study sheds light on the complex interactions between typhoons and marine ecosystems and highlights the importance of further investigating these phenomena to better understand their ecological implications.