Accurate and efficient prediction of deformation and residual stress in large metal components manufactured through wire-arc directed energy deposition is essential for optimizing the process parameters and ensuring the quality of the components. The finite element method (FEM) together with the inherent strain concept is a promising approach to solve the problems, but its prediction accuracy requires improvement, especially for the prediction of the residual stress. Motivated by this, a process-based inherent strain method (PISM) is proposed, which can better reflect the layer-wise process of wire-arc directed energy deposition. For one thing, an accumulative effect of the plastic strain, which results from multiple remelting during the sequential deposition process, is taken into account when the inherent strain is calculated and loaded. For another, an additional strain is introduced into the total inherent strain, in order to resolve the continuity conflict of deformation and then to dismiss the unrealistic stress oscillation between the equivalent layers, when a layer lumping method is used. In addition, the idea of decomposing plastic strain into a locally-related part and a structure-related part is proposed, which clarifies the theoretical basis of the inherent strain method for metal additive manufacturing. Numerical examples confirm the necessity for the consideration of the effect of multiple remelting, and the introduction of the additional strain. Comparisons with the predictions by the thermo-elastic–plastic model and the conventional inherent strain method, as well as with the experimental results, verify the validity and accuracy of the present PISM.