Environmental DNA (eDNA) technology was applied to monitor six Apostichopus japonicus cultivation ponds during the summer and autumn of 2023 to investigate the phytoplankton community structure and its impact on the environment in sea cucumber (Apostichopus japonicus) cultivation ponds. The survey results showed that 8 phyla, 103 genera, and 162 species of phytoplankton were detected in the summer, while 8 phyla, 248 genera, and 465 species were recorded in the autumn. The phytoplankton species composition and relative abundance were dominated by Dinoflagellata, Chlorophyta, and Bacillariophyta. A seasonal succession was observed in dominant species, with 41 dominant species identified, mainly belonging to Dinoflagellata, Chlorophyta, and Bacillario phyta. The biodiversity and evenness indices of phytoplankton were lower in summer than in autumn, whereas the richness index was higher in summer. According to biodiversity indices, the A. japonicus cultivation ponds were classified as lightly to moderately polluted during the study period. Redundancy analysis (RDA) of the phytoplan kton community structure and environmental factors revealed that the relative abundances of Bacillariophyta, Dinoflagellata, and Chlorophyta were positively correlated with nitrate concentration, phosphate concentration, and total phosphorus, nitrate, and ammonia nitrogen, respectively. These findings provided a scientific basis for environmental regulation in A. japonicus cultivation.