The invention discloses cellulose aerogel and a preparation method and application thereof. The method includes the steps of firstly, regulating pH of a chitosan solution to 9-10, and adding xylanasefor processing for 20-30 minutes; processing in microwaves for 10-30 minutes, and stirring for 60-120 minutes; adding cellulase for processing for 20-60 minutes to obtain microfiber slurry; adding carboxymethyl cellulose into the microfiber slurry, regulating pH to 6-8, stirring and mixing for 20-60 minutes, and fluidizing in a fluidizer to obtain microfibrillated cellulose; secondly, mixing the microfibrillated cellulose and vinyl trimethoxy silane, regulating pH to 4-5, and stirring for 20-60 minutes; performing freeze drying to obtain the cellulose aerogel. The cellulose aerogel has the advantages that the cellulose aerogel is subjected to silylation modification to allow the surface of the cellulose aerogel to have good hydrophobic property, the contact angle of surface water drops canreach 165 degrees, and the cellulose aerogel can be used for adsorbing oiling agents, oil and the like to perform oil-water separation.