Stiffness identification from measured responses is an important part of structural health monitoring, in which finite element model updating (FEMU) is a widely studied method. However, the practicability of this method still needs to be improved when applied to large deteriorated civil structures. In this paper, a new FEMU strategy based on the PSO (particle swarm optimization)-Kriging model assisted by the Levenberg–Marquardt (LM) algorithm is proposed for the stiffness identification of deteriorated long-span prestressed concrete (PC) continuous girder bridges. The strategy is implemented in two phases: global stiffness identification based on the LM algorithm is adopted in phase I to determine the sampling interval of the identification parameters; then, in phase Ⅱ, the girder is divided into segments, and the accurate value of each segment stiffness is determined. The PSO-Kriging model is employed to facilitate the high accuracy and efficiency of the method. The effectiveness of the proposed method is demonstrated through comparison studies in an existing experiment and a full-scale test, and the parameter selection of the method is also discussed.