The invention discloses organic silicon resin capable of improving water damage resistance of roads as well as a preparation method and application of the organic silicon resin. An organic silicon monomer II and a silane monomer III are reacted in an organic solvent under the action of a metal catalyst; the mol ratio of the organic silicon monomer II to the silane monomer III ranges from (1: 2) to (1: 1); a material obtained by the reaction and epoxy chloropropane are reacted for 2-7 hours under the condition that the temperature is 40-70 DEG C; the dropping speed of the epoxy chloropropane is 30-60 drops/min; and the mol ratio of the silane monomer III to the epoxy chloropropane ranges from (1: 2) to (1: 1). The preparation method of the organic silicon resin capable of improving the water damage resistance of the roads is simple in synthesis process, moderate in reaction conditions and relatively high in yield; the obtained organic silicon resin can be used for effectively improving the water damage resistance performance of an asphalt mixture and the freeze-thaw split strength ratio reaches more than or equal to 95%; the synthesized organic silicon resin adopts the metal catalyst and is green and environmentally friendly; and when the organic silicon resin is used for preparing the asphalt mixture, the road performance of the mixture is guaranteed.