Abstract: For feeder container ship transportation with the characteristics of changeable feeding ports and variation of berthing conditions at ports, a two-stage method is applied to jointly optimizing route planning and cargo stowage of the feeder container ships. With the constraints of ship capacity, ship stability and cargo delivery time, a MIP（Mixed Integer Programming） model is constructed for the objective of minimizing the total operating cost of the container fleet and minimizing the number of mixed stacks. A PSO（Particle Swarm Optimization） algorithm is designed to solve the problem. Several practical cases are calculated to demonstrate the efficiency difference between direct model calculation and the PSO algorithm. For larger scale problems, the solution time for model direct calculation exceeds 600 s, while with PSO, the maximum solution time is 16.66 s and the average solution time is 10.00 s. Which can provide reference for practical optimization of feeder container ship transportation.