The invention relates to a method for preparing silica modified by a silane coupling agent. The method comprises the following steps: preparing a kind of coupling agent sol solution by mixing the solvent, water, catalyst and coupling agent; uniformly dispersing silica into the sol solution by means of ultrasonic dispersion or shear dispersion to achieve a turbid solution with uniform dispersion and ideal particle size; and then stirring the turbid solution at a constant speed to make the coupling agent sol reacting with silica to prepare highly hydrophobic silica modified by the coupling agent through controlling the temperature and reaction time. The coupling agent sol solution is obtained by a sol-gel process and silica is uniformly dispersed in the coupling agent sol solution through combined action of various dynamic means to ensure the sufficient reaction between silica and coupling agent, thus to obtain silica modified by the coupling agent.