The invention relates to a method for preparing microcapsule through miniemulsion polymerization by utilizing a siloxane copolymer as an auxiliary stabilizing agent, belonging to the field of emulsion polymerization. The method comprises the following steps: 1, preparing an organic siloxane copolymer with lower molecular weight by a solution polymerization method; and 2, preparing a nano capsule by miniemulsion polymerization by utilizing the organic siloxane copolymer prepared in the step 1 as the auxiliary stabilizing agent, and finally preparing the microcapsule with the particle size of 60-200 nm. In the invention, the organic siloxane copolymer with lower molecular weight serving as the auxiliary stabilizing agent is prepared by the solution polymerization method, thereby avoiding the residue of the traditional auxiliary stabilizing agent in the product; and hydrolysis is carried out in the process of miniemulsion polymerization so as to form a Si-O-Si structure, and finally the hybridized capsule can be prepared, so that the microcapsule can be preferably applied to the fields of paintings, biomedicine and the like.