A method for measuring the internal deposition sputtering of an ion thruster comprises the following steps: (1) an ion thruster is installed in a vacuum system, and a cover plate half-covered with covering is installed at a specified position inside the ion thruster; (2) the ion thruster accumulates guide beam current to work for at least 100h; (3) the ion thruster stops ignition and opens a vacuum chamber, the cover plate is removed, and a protective device covering the cover plate is stripped off; and (4) the thickness difference between the two sides of the cover plate is measured using a step profiler or a 3D contourgraph, the sputtering rate of a vacuum tank per unit time and the distribution area of sputtering materials are calculated out according to the ignition time of the thruster, and composition detection is performed through an X-ray photoelectron spectroscopy analyzer or an energy spectrum analyzer to determine the source of sputtering materials. Through the method, the sputtering sources of deposits at different positions inside a thruster can be judged, and the sputtering yield and wear rate of the core parts can be analyzed in a half-quantitative manner. The method is used to verify a sputtering model of the discharge chamber of an ion thruster, and also can be used to estimate the service life of an ion thruster under the condition of continuous work.