Microscopic propagules of Ulva species (UMPs) spread on Subei Shoal are believed to play a significant role in the formation of the Yellow Sea green tide. Previous laboratory and ship-based studies indicated that modified clay (MC) can effectively remove UMPs from the water column and restrict their germination. To evaluate the effectiveness of this method under natural conditions, a mesocosm experiment was conducted on the Zhugensha sandbank on Subei Shoal. The results show that the suspended particles on the sandbank would partially disturb the flocculation process between the MC and UMPs. However, the MC at a proper dose could effectively remove UMPs from the water column and decrease the adhesion and germination of UMPs on the nylon ropes that comprised the mariculture rafts by >75%. This method was proven a potential strategy to restrict the initial biomass accumulation of green algae on Subei Shoal. However, field trials in larger time-space scales are still needed to assess the efficiency of this method when used in the open sea.