The residual stress field induced by surface strengthening processes such as mechanical shot peening and other forms of plastic deformation does not generally exhibit a simple “monotonic” distribution trend. Some researchers have analyzed this fact from a mechanical perspective based on Hertz theory. However, the micro/nano-scale microstructural changes corresponding to the distribution of residual stress fields still appear to be lacking. In this study, we focused on a widely used material in aviation manufacturing, namely nickel-based superalloy GH4169, as our experimental material. We subjected GH4169 alloy to mechanical strengthening treatment using a shot peening intensity of 0.25 mmA, followed by quantitative testing of micromechanical performance indicators such as microhardness and residual stress. To thoroughly investigate the relationship between micromechanical properties and microstructure changes, we utilized transmission electron microscopy (TEM) to observe and analyze shot-peened materials at different depths. Our findings revealed that the most severe microstructural distortion induced by mechanical shot peening in GH4169 alloy was likely to occur within a depth range of 25 to 75 µm. This observation aligns with the actual phenomenon that the maximum microhardness and maximum residual compressive stress did not manifest on the outermost surface of the material. By presenting a detailed analysis of deformation defects such as dislocations, stacking faults, and twinning in different depths of mechanically strengthened layers, our study contributes to a deeper understanding and practical application of post-processing technologies based on plastic deformation.