The invention discloses Ag-doped Mg2Si-based thermoelectric thin film and a preparing method thereof. Double-target cyclic sputtering is carried out on an insulating substrate by a magnetron sputtering deposition process, wherein in one target position, an Mg2Si target is placed, and a radio frequency power supply is used as the power supply; in another target position, an Ag elemental target is placed, and a direct current power supply is used as the power supply; first, an Mg2Si layer is plated, next, an Ag layer is plated, then an Mg2Si layer is plated again, and one period is finished; cyclical sputtering is carried out according to the period for multiple times so as to prepare and obtain thin film with a laminated structure; and finally, the Ag-doped Mg2Si-based thermoelectric thin film is obtained by adopting vacuum annealing. The magnetron sputtering process preparing technology has the advantages of being strong in film layer and substrate binding force, even and dense in film layer, simple in technology, low in cost and the like, and can be used and popularized in the production of preparing the thermoelectric thin film.