The Changjiang estuary (CJE) is a large estuary that is affected by multiple anthropogenic stressors and climate change. The long-term trend of zooplankton in the CJE is an important indicator of the ecological response to stressors. We applied the Mann–Kendall trend analysis and Pettitt test to detect the trend and breakpoints of the biomass of the large mesozooplankton (LMZ; 505–20 000 μm) in four seasons, abundance of main LMZ taxa in summer from the 1960s to 2020, and abundance of dominant species in summer from 2000 to 2020 in the CJE. Results showed that LMZ biomass increased significantly during spring and summer, and the breakpoints both occurred in the 1980s. After the breakpoint, the mean biomass increased from 142.88 to 429.42 mg/m³ in spring and from 296.28 to 723.92 mg/m³ in summer. After 2000, the abundance of Copepoda in summer increased by more than 10 times compared to the 1960s. Under the conditions of warming and increased dinoflagellate abundance in the CJE, the abundance of the warm-water and omnivorous small calanoid copepod Paracalanus aculeatus increased significantly. Meanwhile, the significant decrease in the abundance of the temperate brackish species Labidocera euchaeta was probably mainly related to warming. The rapid changes in LMZ biomass during the late 1980s and mid-1990s is probably the result of a combination of enhanced bottom–up support, reduced top–down pressure, and promotion of temperature. This study provides scientific evidence and insights into the adaptive management of the Changjiang Basin.

长江口（CJE）是一个受多种人为压力和气候变化影响的大型河口。CJE中浮游动物的长期趋势是生态对压力源的反应的重要指标。我们应用 Mann-Kendall 趋势分析和 Pettitt 检验检测了 1960 年代至 2020 年夏季大型中型浮游动物（LMZ；505-20 000 μm）生物量的趋势和断点，夏季主要 LMZ 类群的丰度， 2000-2020年CJE夏季优势种和丰度。结果表明，LMZ生物量在春夏两季显着增加，断点均出现在1980年代。在断点之后，平均生物量在春季从 142.88 增加到 429.42 mg/m ^{3 ，从 296.28 增加到 723.92 mg/m 3}在夏天。2000年以后，桡足类在夏季的丰度比1960年代增加了10倍以上。在气候变暖和 CJE 甲藻丰度增加的条件下，温水型和杂食性小型长颈桡足类的丰度棘轮旁显着增加。同时，温带半咸水物种的丰度显着下降蓝口角鲨可能主要与变暖有关。1980 年代末和 1990 年代中期 LMZ 生物量的快速变化可能是自下而上支持增强、自上而下压力降低和温度升高共同作用的结果。本研究为长江流域的适应性管理提供了科学证据和见解。