The present study considers the transport discounts and capacity constraints for the suppliers and manufacturers simultaneously to provide a multi-objective decision-making model for supplier selection on a three-level supply chain. For this purpose, it begins with presenting a nonlinear mixed-integer model of the problem, where the objectives include the minimization of the logistics costs and lead time. Subsequently, the NSGA-II algorithm is developed to solve the large-scale model of the problem and simultaneously optimize the two objectives to achieve Pareto-optimal solutions. To test the efficiency of the proposed algorithm, several synthetic examples of various sizes are then generated and solved. Finally, the paper compares the performance of the proposed metaheuristic algorithm with the augmented epsilon-constraint method. In summary, the findings of this study provided researchers and industries to easily access to a cohesive model of supplier selection considering transportation that are essential to the solution of many real-world challenging logistics issues.