Harmful algal blooms are a global problem in water environments, and their explosive growth endangers the health of aquatic ecosystems. Magnetic nanomaterials for the harvesting of microalgae have received a lot of attention because of their high efficiency, low cost, and ease of operation. In this study, magnetic mesoporous silica nanomaterials were prepared using Fe3O4 as a carrier and harvesting on Chlorella sp. HQ. It was found that silica coated with magnetic Fe3O4 microspheres has good dispersion. The harvesting of Chlorella sp. HQ via magnetic mesoporous silica could be maintained over a wide pH range (4 to 12). After the removal of organic components from the surface of the material, the magnetic mesoporous silica obtained a better porous structure. The ethanol reflux method was more beneficial than the calcination method in maintaining the stable structure of the material, thus improving the harvesting efficiency of the material for the microalgae Chlorella sp. HQ by a maximum of 17.8% (65.9% to 83.7%). When the molar ratio of active agent cetyltrimethylammonium bromide (CTAB) and stabilizer polyvinylpyrrolidone (PVP) was 1: 0.092 at pH 4 and algal concentration of 0.5 g/L, the materials showed the maximum harvesting efficiency of Chlorella sp. HQ was 84.2%.