The Phaeocystis globosa widely exists in the seawater, which becomes a great threat for the health of humans and animals in the ecological ecosystem. In this work, we reported a promising control strategy with quercetin(QT) enhanced cellulose nanocrystals (CNC). The quercetin enhanced cellulose nanocrystals (QT/CNC) was characterized through Atomic Force Microscopy (AFM), Fourier Transform Infrared Spectrometer (FTIR) and X-ray diffractometer (XRD). The effects of concentrations of CNC and QT on controlled Phaeocystis globosa were investigated. The results showed that the removal rate of Phaeocystis globosa exhibited an optimal value (92.1 %) at 0.05 g L-1 CNC and 0.1 g L-1 QT. Furthermore, the chlorophyll-a content in the Phaeocystis globosa exhibited a remarkable decrease from 3.72 mg L-1 to 0.21 mg L-1 when QT/CNC was interacted. On the basis of these results, we concluded that Phaeocystis globosa could be removed by QT/CNC effectively. During the removal of Phaeocystis globosa, the pH of algal solution decreased from 9.45 to 7.36, indicating that QT/CNC could maintain the normal pH of water. In addition, the testing result of the QT/CNC zeta potentials was negative, which revealed that Phaeocystis globosa was removed through inhibition and flocculation. Accordingly, a possible removal mechanism of Phaeocystis globose by QT/CNC was presumed. This study suggested that QT/CNC might be a potential treatment materials on the removal of Phaeocystis globosa.