The invention relates to a preparation method and applications of a modified water hyacinth algae flocculant, wherein chitosan is used as a modifier, and chitosan and water hyacinth are subjected to mixing treatment to obtain the algae flocculant. The preparation steps comprise: placing fresh root-leaf-removed water hyacinth in an oven, drying and removing water, crushing, screening, mixing the obtained water hyacinth and a chitosan solution, stirring, filtering, drying, and grinding to obtain the modified water hyacinth algae flocculant. According to the present invention, the modified water hyacinth algae flocculant for removing Microcystis during the Cyanobacteria blooms, the preparation method and the applications are provided, the modified water hyacinth algae flocculant can rapidly and effectively remove the Microcystis in the Cyanobacteria blooms, can achieve the emergency treatment on the Cyanobacteria blooms, has advantages of good removing effect, rapid effect and simple operation, and provides the important theoretical and practical significance for the rapid treatment of the Cyanobacteria blooms; and by modifying the water hyacinth around the Cyanobacteria blooms, the long-distance flocculant transportation cost is saved, and the economic benefits are great.