Microcystis aeruginosa (M. aeruginosa) blooms and microplastics pollution have been major global water pollution concern in lakes and reservoirs. In this study, the behaviour of M. aeruginosa–microplastic composite pollutants in inorganic coagulant (PACl) and organic coagulant (HTCC) treatment was investigated. Results showed that, in coagulation stage, the dissolved extracellular polymers secreted by M. aeruginosa could promote the adhesion of microplastics to algae, so as to combine them into the algal flocs, thus improving the sedimentation and removal efficiency of microplastics. On the other hand, whilst microplastics increased the size of algal flocs in PACl coagulation and improved algal removal efficiency, they had the opposite effect on HTCC coagulation. And the removal of algal metabolites including microcystins were improved by the presence of microplastics.In sludge storage stage, the oxidative and mechanical damage effects of microplastics promoted the rupture of M. aeruginosa cells in PACl sludge but not in HTCC sludge, which mean more potential risks in recycling of PACl sludge water. Besides, microplastics promoted the proliferation of beneficial bacteria such as Poterioochromonas and Coccomyxa, which contributed to the control of sludge pollution.