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Microcystis aeruginosa is one of the most famous harmful algae. In this work, Z -scheme g-C 3 N 4 -MoO 3 (Mo-CN) composite photocatalysts were successfully synthesized to alleviate the algae pollution. The obtained composites exhibited excellent performance for the inactivation of M. aeruginosa. The optimal photocatalysts (15Mo-CN) achieved a removal efficiency of 97% for the algal cells after 3 h visible light irradiation, which was attributed to their remarkable surface properties and ingenious structure design. The physiological status of Microcystis aeruginosa were evaluated by the chlorophyll a (chla), relative electron transport rate (rETR) and maximum photochemical efficiency (Fv/Fm), and all of them decreased in different degrees. Furthermore, the as-prepared photocatalysts also show a certain activity for the removal of leaked macromolecule organic compounds during the process of algal cells inactivation. Finally, a possible mechanism on the photocatalytic inactivation of algal cells by the Z -scheme photocatalysts was deduced based on the experimental and characterization results. We believe this study would provide new insights into the development of promising technology and basic theory for remediation of algae pollution. Mediator-free direct Z-scheme g-C3N4-MoO3 composite photocatalysts were controllably synthesized and used to the inactivation of Microcystis aeruginosa for the first time. The obtained composites exhibited excellent performance for the inactivation of M. aeruginosa. The mechanism for the enhanced activity was discussed deeply based on the experimental results. Unlabelled Image • A Z-scheme photocatalyst was successfully prepared for inactivation of M. aeruginosa. • 97% of M. aeruginosa can be inactivated in 3 h visible light irradiation. • The high activity can be ascribed to the Z scheme charge transfer mechanism. • The leaked organic matters can be removed in the inactivation process. [ABSTRACT FROM AUTHOR]