Based on 245 samples collected in 19 cruises from 1960 to 2010 in adjoining waters of the Yellow River estuary, the long-term changes of the phytoplankton community and diversity were analyzed. These samples were towed from the seafloor to the surface at each site by using a standard phytoplankton net and subsequently checked for the species composition and cell abundance under an optical microscope in the laboratory. A total of 108 species were recorded, of which 87 were diatoms and 17 were dinoflagellates. spp. were the larger groups, with 27 and 10 species documented, respectively. The average total phytoplankton abundance during the last fifty years was 2.74×10⁶ ind/m³, with a peak of 16.8×10⁶ ind/m³ in the 1980s. Diatoms dominated the community in the last century, such as the large centric diatoms spp. However, the species in this century shifted to pennate diatoms like , as well as benthic species like . There was an increasing trend in abundance of the dinoflagellates spp. During the past fifty years, Coscinodiscus debilis, and were dominant in the community. However, the composition of dominant phytoplanktons had indeed changed and shifted. Under the co-influence of the absence of river flow and a strong El Niño event, the species abundances and diversity had decreased to the lowest levels during the last century, with average values only being 87.7×10⁴ ind/m³ (Shannon-Weaver index=1.97). During this century, however, the phytoplankton community and diversity in the Yellow River estuary have been altering under human activity, such as water-sediment regulation, with a steady recovery of 2.3 times and 16.8% increase over the levels at the end of the last century. This study on the long-term shift in phytoplankton community and diversity will provide a basic background for future protection of the estuarine ecosystem and enhancement of fishery resources in the adjoining waters of the Yellow River estuary.