The invention relates to a sample preparation method for mice brain tissue proteome analysis. The method comprises the following steps: (1) replacing the blood through apex perfusion, namely, narcotizing a mice, performing slow apex perfusion, stopping while the liver is in grey white, and taking out a brain tissue; (2) extracting protein, namely, grinding the brain tissue into powder, adding a pre-cooled Tris buffer solution, ultrasonically treating, incubating in a shaking table, and centrifuging to obtain a protein extracting solution I; (3) thermally treating to increase protein solubility, namely, mixing the protein extracting solution I and the thermally treated solution, treating for 5min, and centrifuging to obtain the protein extracting solution II; (4) precipitating to remove fat, namely, adding the protein extracting solution II in the pre-cooled fat-removing precipitation solution CUS, precipitating, centrifuging, washing, and drying to obtain purified protein powder; and (5) re-dissolving the protein, namely, adding the purified protein powder in an urea protein lysate, and centrifuging to obtain a proteome sample. With the sample preparation method disclosed by the invention, blood and fat influences of the brain tissue of the mice can be economically and efficiently removed, and the solubility of the protein sample is increased.