Eutrophication has attracted social’s attention as it is a worldwide problem in freshwater aquatic ecosystem. Therefore, cultivation of microalgae in nutrient-rich medium can serve as wastewater treatment as they remove the pollutants from aquatic environment and the microalgal biomass can produce biofuels or other valuable bioproducts. Although microalgae harvesting by gravity sedimentation method is less expensive but it promotes slow sedimentation rate and increases the possibility of biomass deteriorates during harvesting process. In this research, the silica micro-clusters (SMCs) was being synthesized and surface functionalized by positively charged chitosan to improve the attachment with microalgal cells in order to promote rapid microalgae removal through sedimentation. The cell removal efficiency of Chlorella sp. can reach up to 99.41 ± 0.64 % by using 1 g/L of surface functionalized SMCs (SF-Si). Moreover, it also tended to promote high rate of cell sedimentation at 22.71 ± 3.02 cm/h which was about 162 times faster than self-sedimentation. This method of silica-aided-sedimentation (SAS) had proven effective to harvest the multi-species microalgal cells which collected from Tualang lake, Perak, and achieved cell separation efficiency up to 100% by 80 mg/L of SF-Si.