Kriging surrogate model provides explicit functions to represent the relationships between the inputs and outputs of a linear or nonlinear system, which is a desirable advantage for response estimation and parameter identification in structural design and model updating problem. However, little research has been carried out in applying Kriging model to crack identification. In this work, a scheme for crack identification based on a Kriging surrogate model is proposed. A modified rectangular grid (MRG) is introduced to move some sample points lying on the boundary into the internal design region, which will provide more useful information for the construction of Kriging model. The initial Kriging model is then constructed by samples of varying crack parameters (locations and sizes) and their corresponding modal frequencies. For identifying crack parameters, a robust stochastic particle swarm optimization (SPSO) algorithm is used to find the global optimal solution beyond the constructed Kriging model. To improve the accuracy of surrogate model, the finite element (FE) analysis soft ANSYS is employed to deal with the re-meshing problem during surrogate model updating. Specially, a simple method for crack number identification is proposed by finding the maximum probability factor. Finally, numerical simulations and experimental research are performed to assess the effectiveness and noise immunity of this proposed scheme.