To understand the community structure of phytoplankton and its influencing factors in seawater multilevel comprehensive utilization ponds of Yellow River delta, the water environment and phytoplankton status were investigated in May, August and October respectively. The results indicated that 3 phylum and 23 phytoplankton genera were identified, of which 21 genera belonged to Bacillariophyta. Melosira sulcata was the only dominant species in all seasons, and no more than 2 species were 94.29% dominant in water. The richness of phytoplankton was 1.94×105 cells/L with the order of LC>ZY>YZ>JS>TX at different stages of seawater utilization, but there was no significant difference among them (P>0.05). Shannon-Wiener diversity index H’, evenness index J’ and Margalef richness index R were 0.50, 0.33 and 0.52 respectively. At different stages of utilization, for H’ and J, JS > ZY > YZ > LC > TX, and for R, JS > ZY > YZ > TX > LC. The salinity of water increased significantly with the gradual utilization of seawater with the order of JS<YZ<LC<TX<ZY (P<0.05), and pH and dissolved oxygen varied in a contrary trend. The species number of phytoplankton was positively related with pH, dissolved oxygen, richness, water temperature and Shannon-Wiener index (P<0.05) and negatively with salinity (P<0.05). Overall, the biodiversity and evenness of phytoplankton in seawater multilevel comprehensive utilization ponds were lower, and the population was relatively single and influenced by water salinity, water temperature and human disturbance. The results had important significance for improving engineering allocation of different industries (especially aquaculture engineering technology in coastal beach) and production and utilization technology of seawater at different stages of utilization.