Abstract: In order to reveal the changes of plankton community structure during shellfish culture in seawater ponds before and after typhoon, 16S and 18S rRNA genes in the genomic DNA of aquaculture water environment were analyzed by high-throughput sequencing and bioinformatics. The results showed that the number of OTU in prokaryotes (28728) was significantly higher than that in eukaryotes (8498), and the dominant groups of prokaryotes were Proteobacteria, Cyanobacteria, Bacteroidetes, Actinobacteria and Chlorobi; the dominant groups of eukaryotes are ciliates, flagellates, protozoa, cup whipworms, cryptoalgae, Phaeoflagellates, diatoms, etc., among which the diatom abundance increased significantly after typhoon (P<0.05). After the typhoon, biodiversity of eukaryotes did not change significantly, meanwhile the Shannon index and Simpson index of prokaryotes showed significant differences (P<0.05), which decreased in 5d and then increased with time, while the OTU number and Chao I index did not change significantly. The PCoA showed that the community structure of prokaryotic and eukaryotic organisms changed markedly after typhoon. ANOSIM showed that prokaryotic microbial communities were significantly different at each time point (P<0.05), while eukaryotic microbial communities significantly in 10d (P<0.05). Water temperature had a significant impact on prokaryotic community structure (P<0.05), while eukaryotic community was influenced by chemical oxygen demand and phosphat (P<0.05). The study suggested that after the typhoon disturbance, plankton communities markedly changed, prokaryotes was more sensitive than the eukaryotes. The diversity level of bacterial community decreased significantly at first, then returned to the level before typhoon, showing stronger sensitivity than that of eukaryote, and both of them failed to return to the community composition before typhoon. Therefore, the key measures to deal with the impact of typhoon in shellfish culture in seawater ponds should be mainly to prevent cultured organisms from causing stress to the drastic environmental changes, and to supply probiotics for environmental regulation appropriately, so as to make up for the loss of ecological functions possibly caused by the change of bacteria phase caused by typhoon.