Multiple factors and their multi-level effects on the three-dimensional (3D) residual stress field by laser shot peening (LSP) are considered comprehensively, and the model of secondary fuzzy comprehensive evaluation is established based on fuzzy mathematics theory. With such a technical method, the relative merits of residual stress field in LSP by finite element analysis are evaluated, and the fatigue simulation tests of the specimen treated by LSP are done. The fatigue life results show that fuzzy comprehensive evaluation for 3D residual stress field by LSP is effective and feasible. This method will provide guidance for the optimization and control of 3D residual stress field by LSP.