Drifting weeds refer to certain higher aquatic plants and macroalgae that float on the water surface. They typically originate from seagrass beds and macroalgal beds, where large algae are broken off or dislodged by typhoons, waves, or natural abscission during specific growth stages, and are subsequently transported over long distances by wind and currents. When drifting weeds proliferate and accumulate in large quantities, they can trigger ecological disaster events. In recent years, "golden tides" caused by drifting Sargassum horneri have been observed in the East China Sea and the Yellow Sea, with their frequency, scale, and severity showing an increasing trend annually. However, current domestic research on marine ecological anomalies related to macroalgae in coastal waters primarily focuses on the traceability and ecological control of green tides (Ulva prolifera), while studies on the outbreak mechanisms and ecological effects of S. horneri golden tides remain limited. To investigate the impact of golden tides on marine ecosystems and understand the characteristics of nekton community structure in coastal areas affected by drifting weeds, this study was conducted in the coastal waters of Zhoushan, Zhejiang—a major outbreak area of drifting S. horneri in China. In April 2023, bottom trawl surveys were carried out to analyze the diversity of the nekton community in both drifting weed patches and adjacent control areas. Community structure, species composition, resource density, and biodiversity indices were compared between the two areas. A total of 69 nekton species were identified in the survey area, belonging to 12 orders, 37 families, and 59 genera. The total number of species recorded in the drifting weed area and the control area was similar, with 11 orders, 28 families, 45 genera and 54 species in the drifting weed area, and 11 orders, 32 families, 49 genera and 56 species in the control area. Two dominant species were identified in the drifting weed area, compared to one in the control area. The common dominant species in both areas was Lophius litulon. However, significant differences were observed in the size of L. litulon between the two areas. Smaller individuals were more abundant in the drifting weed area, while larger juveniles were more distributed in the control area, suggesting that L. litulon may prefer sheltering within drifting weed litter during early developmental stages. In terms of resource density, the average numerical density (62,194 ind./km2) and biomass density (592.19 kg/km2) of nekton in the drifting weed area were higher than those in the control area (22,461 ind./km2 and 525.1 kg/km2). This indicates that drifting weeds enhance the spatial heterogeneity of surface and bottom waters to some extent, providing favorable aggregation or conservation effects on nekton and functioning similarly to "floating fish reefs" or "benthic fish reefs," thereby positively promoting the conservation of coastal fishery resources. However, it should be noted that the single trawl survey method used in this study only covered the nekton community in the water layer beneath the edge of the algal patches. The aggregation of organisms in this area may be more influenced by the shading effect of floating algae or the attraction of algal litter. The abundance characteristics of nekton within the algal patches require further investigation using more appropriate sampling techniques. Regarding community diversity, the Shannon-Wiener index (2.632) and Pielou’s evenness index (0.660) were higher in the drifting weed area than in the control area (2.136 and 0.531), while the Margalef richness index (6.771) was lower than in the control area (7.421). This suggests that species distribution evenness improved in the drifting weed area, with a more balanced abundance distribution among nekton groups, thereby enhancing overall community diversity. The decrease in species richness in the drifting weed area reflects significant habitat differences between the drifting weed patches and the surrounding waters, which may be closely related to the sheltering effect of drifting weeds and the abundant organic matter provided by algal litter. In conclusion, the presence of drifting weeds in the coastal waters of Zhejiang increases habitat heterogeneity and alters the dominant species composition compared to adjacent areas. The existence of drifting weeds has a positive impact on the diversity of the nekton community structure and the biomass of fishery resources in the affected areas. Therefore, during the harvesting, utilization, or control of drifting weeds, their potential effects on the ecological environment and fishery resource conservation should be fully considered to achieve a balance between resource utilization and ecological protection.