Dissolved algal organic matter (dAOM) originating from harmful algal blooms (HABs) can deteriorate the quality of municipal water supplies, threaten the health of aquatic environments, and interfere with modified clay (MC)-based HABs control measures. In this study, we explored the composition of dAOM from Prorocentrum donghaiense, a typical HAB organism, and assessed the influence of dAOM on MC flocculation. Our results suggested that dAOM composition was complex and had a wide molecular weight (MW) distribution. MW and electrical properties were important dAOM characteristics affecting flocculation and algal removal efficiency of MC. Negatively charged high-MW components (>50 kDa) critically affected algal removal efficiency, reducing the zeta potential of MC particles and leading to small and weak flocs. However, the effect of dAOM depended on its concentration. When the cell density of P. donghaiense reached HAB levels, the high-MW dAOM strongly decreased the algal removal efficiency of MC.