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Phytoplankton distribution in macrotidal estuaries varies strongly due to highly dynamic conditions, contributing to the complexity of aquatic environments and marine ecosystems. Here the Changjiang River Estuary was analyzed as an example to explore this issue, based on field data collected through multiple cruises (including one covering a complete spring‐neap tidal cycle) and a fully coupled hydrodynamics‐sediment‐ecosystem numerical model. The composite analysis of all cruise data clearly showed that the chlorophyll concentrations were relatively low on lunar days 14–17 and 28–2, which corresponded to spring tides. Mechanistic analysis indicated that during spring tides, the river plume front retracts upstream with enhanced vertical mixing. This process restricts the transport of fluvial nutrients while increasing sediment resuspension, and therefore inhibiting net phytoplankton growth. During non‐spring tides, sediment resuspension was reduced but the river plume was further extended with slowed tidal currents, which enhanced the onshore light availability and offshore nutrient conditions and hence stimulated phytoplankton blooms in a larger area. The onshore shifting trend of the chlorophyll maximum region could last till the following neap tide with improved onshore light conditions and activate more conservative nutrients. The non‐conservation of nutrients augments the uncertainty of biomass variations during non‐spring periods. Besides in the spring‐neap tidal cycle, the phytoplankton variability between the perigean and apogean spring tides was also revealed. This study contributes to an improved understanding of intertidal variations of phytoplankton bloom and underlying physical‐sedimentological‐biological coupling mechanisms in tidal estuaries. Plain Language Summary: In macrotidal estuaries, the highly dynamic conditions lead to variations of phytoplankton distribution over multiple time scales, which prompts the complexity of aquatic environments and marine ecosystems. In this study, we explored the intertidal variability of phytoplankton adjacent to the Changjiang River Estuary through multiple observations and a fully coupled hydrodynamics‐sediment‐ecosystem numerical model. An inhibition of phytoplankton accumulation was observed during spring tide, especially during the perigean spring tide. The inhibition is altered during non‐spring tides due to the improvement of phytoplankton growth conditions. It also maintains an onshore shifting trend of chlorophyll maximum region from spring tide to neap tide. However, biomass variations remain uncertain due to the depletion of nutrients. This intertidal variability of phytoplankton is jointly determined by tide‐affected interactions between physical and biological processes. The results contribute to a better understanding of phytoplankton dynamics in global tidal estuaries. Key Points: Phytoplankton accumulation is inhibited during spring tides, especially during perigean spring tidesAn onshore extension trend of chlorophyll maximum regions could last from spring tides to neap tidesTide‐modulated biophysical interactions determine the intertidal variability of phytoplankton [ABSTRACT FROM AUTHOR]