Microcystis aeruginosa is one of the predominant species responsible for cyanobacterial-harmful algal blooms (Cyano-HABs) in water bodies. Cyano-HABs pose a growing number of serious threats to the environment and public health. Therefore, the demand for developing safe and eco-friendly solutions to control Cyano-HABs is increasing. In the present study, the adsorptive strategy using chitosan was applied to remove M. aeruginosa cells from aqueous phases. Using a simple immobilization process, chitosan could be fabricated as a fiber sorbent (chitosan fiber, CF). By application of CF, almost 89% of cyanobacterial cells were eliminated, as compared to those in the control group. Field emission scanning electron microscopy proved that the M. aeruginosa cells were mainly attached to the surface of the sorbent, which was correlated well with the measurement of the surface area of the fiber. We tested the hypothesis that massive applications of the fabricated CF to control Cyano-HABs might cause environmental damage. However, the manufactured CF displayed negligible toxicity. Moreover, we observed that the release of cyanotoxins and microcystins (MCs), during the removal process using CF, could be efficiently prevented by a firm attachment of the M. aeruginosa cells without cell lysis. Our results suggest the possibility of controlling Cyano-HABs using a fabricated CF as a non-toxic and eco-friendly agent for scaled-up applications.