The invention discloses a novel perfluoropolyether alkoxy silane compound and a synthesis method thereof. The structure of the compound is shown as formula (1). The synthesis method includes: reacting hydroxyl terminated perfluoropolyether (PFPE), 3-(2-aminoethyl)aminopropyltrimethoxysilane, 3-(2, 3-epoxypropoxy)propyltrimethoxysilane (KH560), and an HDI trimer in a molar ratio of 1:2:2:1, during reaction, employing a certain amount of a solvent to dilute the mixed hydroxyl terminated perfluoropolyether and 3-(2-aminoethyl)aminopropyltrimethoxysilane, then adding the HDI trimer dropwise, carrying out reaction for 6h at certain temperature, then adding KH560 dropwise, and carrying out reaction for 6h again at certain temperature then reducing pressure and removing the solvent, thus obtaining the perfluoropolyether alkoxy silane compound. The compound can be coated on glass, plastic, film, and other substrate surfaces, and after crosslinking and curing, a layer of solid film can be formed, and the substrate is endowed with excellent anti-fingerprint and antifouling performance and abrasion resistance.