The existing elevation design method cannot adapt to automated container terminals with high-value equipment and high-value stacked goods due to the low elevation design standard for the terminal and the landside and the poor anti-waterlogging capacity provided by the elevation design of the yard. To solve the above problem，this paper analyzes the characteristics of the automated horizontal transport equipment and the containerized goods，summarizes the factors considered by the existing elevation design method and the optimization direction for its application to automated container terminals，and proposes an optimal elevation system design method suitable for automated container terminals. The actual case verification shows that the proposed method can effectively improve the flood control standards of the terminal and the landside and the anti-waterlogging capacity of the yard. Moreover，it can reduce the dumping of dredged soil and thereby save the project investment.