Increasing atmospheric CO₂ concentration leads to ocean acidification, which might affect phytoplankton to varying degrees. Phytoplankton in coastal waters may be affected by seawater acidification and alkalization. In this experiment, Thalassoosira punctigera (diatom) was used to investigate its growth, photosynthesis, dark respiration, cell size, chlorophyll a content, biogenic silica content and chlorophyll fluorescence at seven pCO₂ levels (25 μatm, 50 μatm, 100 μatm, 200 μatm, 400 μatm, 800 μatm, 1 600 μatm). The results showed that, compared with 400 μatm, the growth rate and chlorophyll a content in seawater acidification (pCO₂ > 400 μatm) and alkalization (pCO₂ < 400 μatm) treatments were significantly reduced, but the degree of decrease was greater under the condition of alkalization. In addition, cells showed lower photosynthesis rates and maximum quantum yield of PSII (Fv/Fm) and relative maximum electron transport rate (rETRmax) under alkalization conditions. However, there was no significant changes in biogenic silica content and cell size among different pCO₂ levels. We found both seawater alkalization and acidification could inhibit the physiological activities of T. punctigera, and seawater alkalization had much more inhibited effects. Our results showed that the cell grown at current pCO₂ level (400 μatm) had the optical physiological performance. Moreover, among the pCO₂ levels set in this study, seawater alkalization has a more significant effect on T. punctigera. The present study provides a theoretical basis for studying the effects of changing seawater carbonate chemistry on the marine primary productivity in coastal waters.