Harmful algal blooms are increasingly prevalent globally, posing significant threats to water safety and ecological health. In this study, a novel positive charged buoyant cenosphere (FABC@CTS) was developed for capturing and floating algal cells using chitosan (CTS) and an easily available waste material—fly ash buoyant cenospheres (FABC). The prepared cell-capturing buoyant cenospheres were characterized by various analytical techniques and tested for the removal of Microcystosa aeruginosa. The results demonstrated that at a FABC-to-CTS mass ratio of 8:1 and an FABC@CTS dosage of 55.5 mg CTS/g algae, the removal efficiency of Microcystis aeruginosa exceeded 95%. XDLVO analysis indicated a significant reduction in the repulsive energy barrier after surface modification due to stronger electrostatic and van der Waals forces. Compared with 108 μm buoyant cenospheres, 50 μm FABC@CTS exhibited higher affinity to algal cells, significantly improved the compactness and floatability of aggregates, enabling the rapid flotation of microalgae in 1 min. The FTIR and XPS analysis results further revealed that the amino and hydroxyl functional groups on the surface of the FABC@CTS could effectively capture microalgae through hydrogen bonding and π–π bonding. Overall, the results of this study provide new insights into developing cost-effective and eco-friendly material for efficiently controlling cyanobacterial blooms and contribute to advancing the comprehensive utilization of fly ash solid waste.