The increase of container shipment causes higher demand on the seaport container terminals, container logistics and management. How to rationally allocate the limited space resources and how to improve operational efficiency, is an important subject for container terminals. In this paper, the mathematical modeling and optimization on yard allocation planning based on the mixed storage is proposed with an objective to balance the workload among different blocks and to minimize the delay of container ships. Two corresponding heuristic algorithms are developed to solve this problem. The experimental results show that the proposed algorithms are the promising tool for allocating blocks’ workload.