Powder metallurgy Ni-based superalloy turbine discs serve at high temperatures and high stress levels for a long time, and the comprehensive mechanical properties of the superalloy have stringent requirements, while the surface morphology and microstructure have a significant impact on the performance of the superalloy, which generally requires surface shot peening treatment. Based on this, this work systematically investigates the surface/subsurface microstructure and deformation of the FGH4113A superalloy at different shot peening intensities and explores the quantitative relationship between them. The result indicates that the dislocation pile-up occurs in the subsurface and induces the formation of deformation twins. Meanwhile, the number of deformation twins rises with the increase in shot peening intensity. Furthermore, the dislocations triggered by shot peening induce a large number of low angular grain boundaries in the deformed layer, which results in grain refinement to reinforce the superalloy hardening effect. In addition, with the increase of shot peening intensity, the characteristics of superalloy surface roughness, surface residual compressive stress, hardened layer thickness, and surface microhardness display an increasing trend and exhibit a good linear or power exponential relationship. This finding can provide data to support the regulation of shot peening parameters in the actual production process.