In this work, the influences of shot peening (SP) on ultra-high strength steel were investigated. For the characterization of the strengthened layer, an inclined specimen was proposed for X-ray diffraction and nanoindentation, the micro-mechanical properties in the strengthened layer were studied with both experimental and crystal plasticity finite element (CPFE) analysis. It's noted that SP introduced grain refinement and compressive residual stress were highly concentrated in the surface layer due to the high strength and hardness, and the maximum depth influenced was only 0.1 mm. Based on simulation results, it's found that the differences in nanoindentation loading curves were introduced by the work done by residual stresses. To estimate the residual stress in the strengthened layer, a modified model was proposed with nanoindentation. The newly proposed model gives improved estimation accuracy compared with Wang's model, and it could give more precise results in contrast to the X-ray diffraction method for strengthened layers.