A method of in-situ TEM nanoindentation for a damaged layer of silicon is disclosed. Wet etching and ion beam lithography are used for preparing a silicon wedge sample. An etched silicon wedge is thinned and trimmed by a focused ion beam; thinning uses ion beam of 30 kV: 50-80 nA, and trimming uses ion beam of 5 kV: 1-6 pA; and the top width of the silicon wedge is 80-100 nm. The sample is fixed on a sample holder of an in-situ TEM nanomechanical system by using a conductive silver adhesive. The sample is indented with a tip in the TEM, so that the thickness of the damaged layer of the sample is 2-200 nm; and an in-situ nanoindentation experiment is conducted on the damaged layer of the sample in the TEM.