In response to the problem of solving difficulties caused by multi-constraints and strong coupling in the planning of echelon delivery for amphibious assault formations, a planning method based on a “wave allocation-loading allocation” bi-level programming model is proposed. The characteristics of the planning problem of echelon delivery for amphibious assault formations are analyzed to clarify the planning requirements. A general planning model is established, and based on the bi-level programming idea, wave allocation and loading allocation models are respectively established. For the upper-level wave allocation model, the genetic algorithm is improved by proposing a guiding mutation operator to enhance the global search capability of the algorithm. For the lower-level loading allocation model, heuristic strategies are designed to improve the solving efficiency of the greedy algorithm. Finally, a complete method for planning the echelon delivery of amphibious assault formations is formed. Combined with typical scenarios of echelon delivery for amphibious assault formations, the AnyLogic system is used for simulation verification. The results show that the planning method is feasible and the results are reasonable, which has reference significance for the decision-making of echelon delivery of amphibious assault formations.