Modal frequencies are often used in structural model updating based on the finite element model, and metamodel technique is often applied to the corresponding optimization process. In this work, the Kriging model is used as the metamodel. Firstly, the influence of different correlation functions of Kriging model is inspected, and then the approximate capability of Kriging model is investigated via inspecting the approximate accuracy of nonlinear functions. Secondly, a model updating procedure is proposed based on the Kriging model, and the samples for constructing Kriging model are generated via the method of Optimal Latin Hypercube. Finally, a typical frame structure is taken as a case study and demonstrates the feasibility and efficiency of the proposed approach. The results show the Kriging model can match the target functions very well, and the finite element model can achieve accurate frequencies and can reliably predict the frequencies after model updating.