In order to analyse the effect of seaweed on zooplankton community structure and its fecal carbon flux, a morphology-based survey of zooplankton community structure was carried out in the Sargassum beds and its adjacent waters of Weizhou Island, Guangxi, in March, May and June 2024, and zooplankton fecal carbon flux was also estimated. In May 2024 when Sargassum bloom, the zooplankton community structure was examined by two types of environmental DNA metabarcoding (18S rDNA and COI gene). A total of 45 zooplankton species, including 38 copepods, were identified by morphology during the survey period. The zooplankton abundance varied from 1160 to 3960 ind. m-3, with the zooplankton species and abundance identified in the Sargassum beds being higher than that of its adjacent waters (P < 0.05). There were large differences in the composition of zooplankton species identified by morphology, 18S rDNA and COI gene, with more copepods identified by morphology, more ciliates detected by 18S rDNA, and more medusa species detected by COI gene. The species detected by all three methods was Temora turbinata. Zooplankton fecal carbon flux varied from 0.215 to 0.574 mg C m-2 d-1, and the zooplankton fecal carbon flux in the Sargassum beds were higher than that in its adjacent waters. The results showed that the growth of Sargassum can improve zooplankton diversity, increase the stability of zooplankton community structure, and increase zooplankton fecal carbon flux.