Huge warship material transfer support operation is one of the critical factors affecting the comprehensive combat effectiveness of warships, which need to deliver essential combat materials to the target position quickly and safely. In this paper, considering the multi-stage and high dynamic characteristics of huge warship material transfer support, we model the operation scheduling optimization problem as a special flexible flow shop scheduling problem with some constraints. A greedy genetic algorithm based on dual-layer integer-coded is proposed to solve the transfer support model with the objective function of minimizing the maximum transfer completion time. Benchmark computation examples and a simulation environment are used in experiments, which verify the effectiveness of the algorithm in the actual transfer support operation.