In order to investigate the effect of shot distance and impact sequence on the residual stress distribution of 42CrMo steel in shot peening (SP) finite element (FE) simulation, 3D dynamic models with order dimple pattern and stochastic dimple pattern were established via ABAQUS/Explicit 6.14, and the simulation results were compared with experiments. The results show that shot overlap has a significant effect on the residual stress distribution of peened parts. Meanwhile, there is a threshold (related to SP parameter) for shot distance in the vertical and horizontal directions. When the shot distance is greater than the threshold in this direction, the residual stress distribution after SP tends to be stable. The impact sequence has almost no effect on the impact of a small number of shots, but this effect will appear when the number of shots increases. It is necessary to avoid shot overlap and continuous impact of adjacent dimples when the FE model is established; on this basis, the distance between shots and the number of layers of the shots can be reduced as much as possible without affecting the residual stress distribution. In addition, the comparison of simulation and experimental results shows that the residual stress evaluation area consistent with the experimental measurement is essential to obtain accurate residual stress distribution in the FE simulation process.