The invention discloses a preparation method of rice hull charcoal and silicon dioxide core-shell double-phase composite filler, comprising the steps of 1), charring dried rice hull in the atmosphere of N2 to obtain rice hull charcoal mixture; 2), ball-milling the rice hull charcoal mixture, and adding to hydrochloric acid solution for acid soaking and stirring; centrifugally washing with distilled water to neutrality to obtain charcoal residue; 3) adding NaOH solution to the charcoal residue; 4), adding hydrochloric acid solution having a concentration of 7% into reacted material, adjusting pH, stirring for reacting, centrifugally washing with distilled water to neutrality, and drying; 5), adding a modifier, and ball-milling to obtain the modified rice hull charcoal and silicon dioxide core-shell double-phase composite filler. The filler prepared by using the method of the invention provides significant improvement in physical and mechanical properties of a rubber composite, improved added value of use for rice hull and effectively reduced environmental pollution.