Rockfill dams are among the most complex, significant, and costly infrastructure projects of great national importance. A key issue in their design is the construction stage and zone optimization. However, a detailed flow shop construction scheme that considers the opinions of decision makers cannot be obtained using the current rock-fill dam construction stage and zone optimization methods, and the robustness and efficiency of existing construction stage and zone optimization approaches are not sufficient. This research presents a construction stage and zone optimization model based on a data-driven analytical hierarchy process extended by D numbers (D-AHP) and an enhanced whale optimization algorithm (EWOA). The flow shop construction scheme is optimized by presenting an automatic flow shop construction scheme multi-criteria decision making (MCDM) method, which integrates the data-driven D-AHP with an improved construction simulation of a high rockfill dam (CSHRD). The EWOA, which uses Levy flight to improve the robustness and efficiency of the whale optimization algorithm (WOA), is adopted for optimization. This proposed model is implemented to optimize the construction stages and zones while obtaining a preferable flow shop construction scheme. The effectiveness and advantages of the model are proven by an example of a large-scale rockfill dam.