Large welding-induced distortions are inevitably generated in a thin-plate welded joint due to its weak stiffness. In this study, an equivalent thermal strain method based on inherent strain theory is proposed to predict the welding deformation of thin plates. An artificial temperature and an orthotropic thermal expansion coefficient are adopted to directly simulate the welding shrinkage and bending behavior of the cooling phase in all directions. To describe the distribution of transverse inherent strain through thickness more accurately, a composite shell element is employed, which can divide the thickness into multiple layers and set different material properties. A three-dimensional (3D) thermo–elastic–plastic finite element method (TEP-FEM) model is also developed to simulate the welding process of a thin plate and compute the inherent strain. Moreover, an experiment was performed to verify the accuracy of the numerical model. Comparing the results from experimental data, TEP-FEM, and the proposed method, it is discovered that the new method can predict the deformation of a thin-plate welded joint with good computational accuracy.