The precipitate morphology in Mg–rare earth (RE) element binary alloys is predicted using a multi-scale modeling approach combining a three-dimensional (3-D) phase-field model and first-principles density functional theory calculations. First-principles calculations provide all the required input parameters for the phase-field model, including lattice parameters, elastic constants, formation energies and interfacial energies. This integrated model is applied to a Mg–Nd alloy as a model system. Quantitative 3-D phase-field simulations are performed to study the metastable β′ precipitate morphologies, habit plane formation and spatial distribution of the precipitates during isothermal aging. The predicted morphologies of β′ precipitates are in excellent agreement with existing experimental observations. The influence of the precipitate morphology on the mechanical properties is also evaluated using the Orowan equation. The results are expected to provide guidance for achieving desirable precipitate morphologies and thus mechanical properties in Mg alloys.