Aero engine compressor disks are typically life-limited parts and it is necessary to secure them through the implementation of an engineering plan and a manufacturing plan. Specifically, the engineering plan recommends the quantification of the safety of life-limited parts on the basis of probabilistic risk assessment (PRA). However, the direct correlation between plans is limited, and the effect of manufacturing parameters on the safety of life-limited parts remains to be investigated. Shot peening, as a typical method of surface manufacturing, can significantly improve the safety of life-limited parts. Therefore, a modified mathematical surface PRA method considering shot peening parameters is developed in this paper to further bridge the design and manufacturing processes. Additionally, a general database is established using the response surface method to overcome the simulation complexity. On the basis of this method and the general database, an innovative direct and efficient determination of key shot peening parameters through failure risk in the design stage is proposed. The results indicate that failure risk decreased by 3.26%, 11.31%, and 9.71%, respectively, with increasing number, diameter, and velocity of shots, with the effect of diameter being the greatest. In addition, the method improves the efficiency of determining the key parameters by 75.80%, thus satisfying the requirements of abundant and efficient iterations during the design stage.