During bridge service, material degradation and aging occur, affecting bridge functionality. Bridge health monitoring, crucial for detecting structural damage, includes finite element model modification as a key aspect. Current finite element-based model updating techniques are computationally intensive and lack practicality. Additionally, changes in loading and material property deterioration lead to parameter uncertainty in engineering structures. To enhance computational efficiency and accommodate parameter uncertainty, this study proposes a Gaussian process model-based approach for predicting structural natural frequencies and correcting finite element models. Taking a simply supported beam structure as an example, the elastic modulus and mass density of the structure are sampled by the Sobol sequence. Then, we map the collected samples to the corresponding physical space, substitute them into the finite element model, and calculate the first three natural frequencies of the model. A Gaussian surrogate model was established for the natural frequency of the structure. By analyzing the first three natural frequencies of the simply supported beam, the elastic modulus and mass density of the structure are corrected. The error between the corrected values of elastic modulus and mass density and the calculated values of the finite element model is very small. This study demonstrates that Gaussian process models can improve calculation efficiency, fulfilling the dual objectives of predicting structural natural frequencies and adjusting model parameters.