The present invention relates to a high-temperature resistant modified silicon-containing cyanate ester resin as well as a preparation method and an application thereof. The preparation method comprises the following steps: adding a mixed solution of hydroxyl silicone oil, a silane coupling agent and an organic solvent into a mixed solution of a tetramethylammonium hydroxide aqueous solution and a polar solvent, performing hydrolytic polycondensation at a temperature of 5-40° C. for 4-8 h, and performing distillation to obtain an epoxy-containing silsesquioxane; performing pre-polymerization on the epoxy-containing silsesquioxane and a cyanate ester resin at a temperature of 50-100° C. for 1-8 h to obtain a modified cyanate ester resin; and uniformly mixing the modified cyanate ester resin and a modified anhydride, thereby obtaining the high-temperature resistant modified silicon-containing cyanate ester resin.