The invention provides a preparation method of a functionalized polyhedral oligomeric silsesquioxane-titanium dioxide composite aerogel. The preparation method comprises the following steps: 1, pre-hydrolyzing a polyhedral oligomeric silsesquioxane monomer of a silicon-based triethoxy vinyl group under the action of an acid as a catalyst; 2, adding a titanium precursor solution to a weakly-acidic alcohol solution of the pre-hydrolyzed functionalized polyhedral oligomeric silsesquioxane monomer obtained in step 1 for a hydrolysis-condensation reaction; and 3, gelating the wet gel obtained in step 2, ageing, carrying out solvent exchange, and carrying out carbon dioxide supercritical drying to obtain the functionalized polyhedral oligomeric silsesquioxane-titanium dioxide composite aerogel. The method has the advantages of no addition of a metal complexing agent or a polymer, simple synthetic preparation of the above raw material, mild sol-gel condition, and controllable preparation technology; and the obtained aerogel has the advantages of high specific surface area, narrow aperture distribution at nanometer level, and uniform and stable structure, and can be widely applied to the adsorption field, the catalytic field and the like.