The invention discloses aqueous polysiloxane resin and a preparation method thereof. The aqueous polysiloxane resin is prepared from a pre-emulsion A, an emulsion B and a solution C as raw materials. The preparation method comprises the following steps: 1) preparing the pre-emulsion A; 2) preparing the emulsion B; 3) preparing the solution C; 4) pouring a part of the pre-emulsion A into a reaction container, dripping a part of the emulsion B, and at the same time heating the reaction container to 55-65 DEG C to react for 0.5-1 hour so as to prepare a light blue fluorescent seed emulsion; 5) simultaneously dripping the rest pre-emulsion A and the emulsion B into the fluorescent seed emulsion, heating to 55-65 DEG C to react for 2-3 hours, after the reaction is completed, cooling to the room temperature, adjusting the pH value to be 7-8, dripping the solution C, stirring for 10-30 minutes, and filtering, thereby obtaining a filtrate, that is, the aqueous polysiloxane resin. The aqueous polysiloxane resin is good in storage stability and flexibility, good in adhesion property, high in hardness and good in impact resistance, water resistance, salt water resistance, artificial aging resistance and chemical corrosion resistance. The aqueous polysiloxane resin is simple in preparation method, gentle in reaction condition and stable in process procedure.