In order to solve the problem of berth resource allocation and ship loading in marine loading operation, a method of marine loading project optimization based on bi-level programming was proposed. According to the main characteristics of marine loading project optimization, a solving framework of marine loading problem based on bi-level programming was built. The problem of berth resource allocation on the upper level and the problem of ship loading on the lower level were modeled and solved respectively. A mechanism of result feedback on the lower level and allocation strategy update on the upper level was built. And the experiment and analysis were carried out with the data of Normandy Landing Operations. The analysis result shows that the method has high efficiency and good stability, and it can effectively solve the problem of marine loading project optimization.