The invention provides a method for preparing silicon-based biolubricant base oil from organosilicon modified fatty acid ester. The method comprises the following specific steps: mixing fatty acid ester with organic acid and a catalyst and adding the mixture into an epoxidation reaction kettle, dropwise slowly adding an oxidizing agent, reacting, standing for layering, fetching a supernatant liquid and distilling to obtain epoxidized aliphatic ester; carrying out a ring-opening reaction between epoxidized aliphatic ester and organic acid, washing to neutral level after the reaction and carrying out reduced pressure distillation to obtain a ring-opening product; stirring the ring-opening product and heating to reaction temperature, dropwise adding organosilicon and an acid binding agent according to requirements and carrying out a silylation reaction, directly carrying out reduced pressure distillation after the reaction, and separating a solid to obtain the silicon-based biolubricant base oil. By the above method, the disadvantage that biolubricant base oil produced by existing technologies has poor oxidation stability and poor viscosity-temperature characteristic is overcome. The production process is environment-friendly, and energy consumption is low. The industrial acid binding agent used in the method is low-cost such that cost of the product is reduced.