In this paper, the structural stability of graphene and Mexene was compared by peak force tapping mode of AFM. When in-situ scanning of two-dimensional material of reduced graphene oxide (rGO), the morphology of rGO did not change with time, which indicated that peak force tapping mode had no damage effect on the stable structure surface; while when in-situ scanning of two-dimensional material V2C, nano-etching occurred on the surface of V2C, and the morphology surface area decreased with scanning time. The data processing software was used to analyze the area change and calculate the nano etching rate. It was found that the average nano-etching rate increased with the increase of the peak force, and the etching rate in the atmospheric environment was higher than that in the glove box (Ar atmosphere, the H2O and O2 content was less than 1 ppm), which indicated that the moisture in the atmosphere had an impact on the stability of the material and would accelerate the nano-etching. This study shows that the peak force tapping mode of AFM can be used to qualitatively characterize the stability of two-dimensional materials