Using marine organism monitoring data in Changjiang estuary in the past 15 a, biodiversity dynamics and ecosystem health were evaluated in this study. The results showed that (1) comparing with the late 1990s, the species number of phytoplankton decreased but zooplankton and benthos increased. Diatomophyceae was the largest proportion of the total phytoplankton species and its species ratio was also increased till 2010. Copepoda always plays an indispensable role in zooplankton community but its species ratio decreased alarmingly in this study. Number of Benthos increased during the past 15 a and exceeded 100 from 2015-2018. (2) In a long time, the biodiversity was at a low level. The Shannon-Weaver index of phytoplankton was not as high as expected. Compared with phytoplankton, the values of diversity and evenness of the zooplankton were higher than that of phytoplankton but it decreased during the research time. The diversity of benthos was at a relatively low level and the dominant species were lower than before. (3) The average health index was 21.9 and the estuarine ecosystem was determined as "sub healthy" according The Guidance for the Assessment of Coastal Marine Ecosystem Health (HY/T 087-2005). The factors that influence the biodiversity of the Changjiang estuary include density of phytoplankton, zooplankton and benthos, and biomass of zooplankton and benthos. Factors influenced ecosystem health included sewage discharge, ration of N/P and Si/N, eutrophication etc. The riverine inorganic nitrogen and oil loads to the sea were negatively correlated with health index (P < 0.05). The riverine inorganic phosphorus loads to the sea was negatively correlated with benthos biomass while ratio of N/P was correlated negatively with phytoplankton density but positively with phytoplankton diversity and evenness. Ratio of Si/N correlated negatively with phytoplankton diversity while the factor of eutrophication area was positively correlated with the Diatomophyceae and Dinophyceae species ratio.