The turbidity maximum zone (TMZ) is a distinctive aquatic environment marked by consistently higher turbidity compared to upstream and downstream section. In the TMZ, physicochemical properties such as intense light limitation, abundant nutrients, and rapid salinity shifts play a crucial role in shaping phytoplankton dynamics. The Qiantang River estuary-Hangzhou Bay (QRE-HZB) is a macrotidal estuary system known for its exceptionally high suspended solids concentration. To investigate the impact of TMZ on the standing crop and size structure of phytoplankton in the QRE-HZB, we conducted three cruises in dry, wet, and dry-to-wet transition seasons during 2022-2023, by assessing parameters including size-fractionated chlorophyll a (chl a), turbidity, Secchi depth, temperature, salinity, nutrients, and mesozooplankton. Results reveal significant variations in the TMZ and associated environmental factors in different periods, which markedly influenced the phytoplankton chl-a concentration, size structure, and cell activity (pheophytin/chl a). The chl-a concentration was high with micro-phytoplankton predominance in wet season, while nano-phytoplankton dominated in dry season. Within the TMZ, lower chl-a concentrations and pico-chl-a contributions, alongside higher pheophytin/chl-a and micro-chl-a contributions, were observed. The Spearman's rank correlation and generalized additive model analyses indicated strong correlations of chl-a concentrations with turbidity, nutrients, and mesozooplankton. Redundancy analysis further revealed that salinity, nutrients, and turbidity significantly regulated variations in size structure. Phytoplankton mortality within the TMZ was primarily driven by high turbidity and salinity fluctuations, reflecting the vigorous resuspension and mixing of freshwater and seawater in the QRE-HZB. These findings highlight that the standing crop and size structure of phytoplankton were strongly regulated by the TMZ and associated physicochemical factors in the macrotidal QRE-HZB.