Anthropogenic CO<sub>2</sub> emissions and their continuous dissolution into seawater lead to seawater <em>p</em>CO<sub>2</sub> rise and ocean acidification (OA). Phytoplankton groups are known to be differentially affected by carbonate chemistry changes associated with OA in different regions of contrasting physical and chemical features. To explore responses of phytoplankton to OA in the Chinese coastal waters, we conducted a mesocosm experiment in a eutrophic bay of the southern East China Sea under ambient (410 μatm, AC) and elevated (1000 μatm, HC) <em>p</em>CO<sub>2</sub> levels. The HC stimulated phytoplankton growth and primary production during the initial nutrient-replete stage, while the community diversity and evenness were reduced during this stage due to the rapid nutrient consumption and diatom blooms, and the subsequent shift from diatoms to hetero-dinoflagellates led to a decline in primary production during the mid and later phases under nutrient depletion. Such suppression of diatom-to-dinoflagellate succession occurred with enhanced remineralization of organic matter under the HC conditions, with smaller phytoplankton becoming dominant for the sustained primary production. Our findings indicate that, the impacts of OA on phytoplankton diversity in the coastal water of the southern East China Sea depend on availability of nutrients, with primary productivity and biodiversity of phytoplankton reduced in the eutrophicated coastal water.