An accurate finite element model (FEM) plays a critical role in the structural damage identification. However, due to the existence of the uncertainties, such as material properties and modeling errors, it always exists some gaps between the analytical FEM and experimental structure. While an artificial neural network (ANN)-based model updating methods have been widely adopted to narrow the gap and obtain a baseline FEM, it still faces inaccurate results and fails to meet the physical law. In this regard, the study proposes a novel physics-based loss function inspired by modal sensitivity analysis and incorporates it into the residual neural network, thereby forming a novel physics-guided neural network (PGNN) method. The mapping relationship between the input of structural responses and output of model updating variables is constrained to retain its physical meaning by guiding the training process instead of pure data association, which aims to improve the accuracy of the ANN-based method and achieve accurate and high-efficiency model updating. An experimental example of a continuous rigid frame bridge is adopted to verify the feasibility of the proposed method. Additionally, other common model updating methods, including moth-flame optimization and regularization method, are used to make a comparison. The noise-robustness of the proposed method is investigated as well. Compared to the existing method, the results illustrate that the proposed PGNN method can achieve better model updating and good noise-robustness under high uncertainties, which means the introduction of the physics-based loss function significantly enhances the parameters updating ability of the neural network. The proposed method exhibits high efficiency and promising potential for large-scale bridge structure model updating.