In view of the problems that traditional methods are prone to falling into local optima in the layout optimization of material yards for limited construction sites, and the solution process often ignores environmental and worker path factors, a two-stage method combining reverse optimization and improved NSGA-II is proposed. The method introduces environmental and worker path indicators to participate in the solution, and selects the comprehensive optimal yard location from the Pareto solution set through TOPSIS decision. The results show that the solution can more effectively generate high-quality yard layouts that meet complex constraints, reducing material transfer time by 21.99%, reducing carbon emissions during transfer by 14.88%, optimizing worker path performance indicators by 38.67%, and significantly improving the overall work efficiency. The results also can provide a reference for the layout optimization of materials in limited construction sites.