Artificial freshwater engineering ecosystems (AFwEEs) have attracted more and more attention. Phytoplankton is critical to the fluctuation of water quality in the AFwEEs. However, there is still a major knowledge gap regarding the ecology, composition, and temporal dynamics of phytoplankton assemblage composition in AFwEEs. Hence, an AFwEEs designed base on the submerged macrophytes (i.e., Vallisneria natans, Najas marina, and Potamogeton crispus) and fishes (i.e., Hypophthalmichthys molitrix, Hypophthalmichthys nobilis, and Ctenopharyngodon idellus) was established. The initial purpose for this survey was to conduct almost entire year (April/2019 – December/2019) sampling investigation to explain the interactions and relationship between multifarious environmental indicators and phytoplankton, also for the different phenomenon explanation of composition change in phytoplankton assemblage between AFwEEs and natural water environments. Consequences exhibited the assemblage dynamics of the phytoplankton were significant varied with seasonal succession, in which Cyanophyta dominated the phytoplankton assemblage while the mean relative abundance accounted for 66.4%, and then was Chlorophyta, for 18.8%. Principal component analysis (PCA) demonstrated temporal variation was significant impacted on phytoplankton assemblages. The dominant species, different assemblages, and distribution of phytoplankton were closely related to the dynamic changes of seasonal succession, which might change the composition of phytoplankton assemblage in the FwAEEs. Results of redundancy analysis (RDA) revealed the water temperature, nutrient concentration, DO concentration, and pH value were the main abiotic environmental indicators affecting phytoplankton assemblage. The trend of the four diversity indices indicated the phytoplankton assemblage became more stable in winter while the change extent of that was more significant in summer.