Microalgae is a promising feedstock of biofuel for alternating fossil fuels. The major challenge of microalgal biofuels for commercial applications is in designing an efficient harvesting method with high economic feasibility. In this study, a rapid flocculation-sedimentation harvesting method induced by organosilane-functionalized halloysite flocculant was achieved for Scenedesmus dimorphus harvest. The harvesting efficiency was significantly influenced by the pH of microalgal dispersion and the dosage of flocculant. The optimized harvesting condition was pH 3.0 with flocculant dosage of 1.0 g.g(-1) cell dry mass. Under the optimized harvesting condition, microalgae rapidly reached 93% harvesting efficiency within 0.5 min of settling time, and reached 98% harvesting efficiency within 2 min of settling time. The rapid flocculation was attributed to the charge neutralization of the negatively-charged microalgae cells by the positively-charged organosilane-functionalized halloysite flocculant and to the sweep flocculation by organosilane-functionalized halloysite flocculant. The organosilane-functionalized halloysite flocculant did not affect the lipid extraction of microalgae, and not contaminate the extracted residuals. The organosilane-functionalized halloysite flocculant is of high efficient, cost-effective, and eco-friendly, makes it be of promising application for commercial microalgae harvesting.