Purpose: The following investigation aims to deal with the competitive relationship among different warehouses & ports in the same company. Design/methodology/approach: In this paper, Game Theory is used in carrying out the optimization model. Genetic Algorithm is used to solve the model. Findings: Unnecessary competition will rise up if there is little internal communication among different warehouses & ports in one company. This paper carries out a novel optimization method on warehouse & port logistics operation model. Originality/value: Warehouse logistics business is a combination of warehousing services and terminal services which is provided by port logistics through the existing port infrastructure on the basis of a port. The newly proposed method can help to optimize logistics operation model for warehouse & port enterprises effectively. We set Sinotrans Guangdong Company as an example to illustrate the newly proposed method. Finally, according to the case study, this paper gives some responses and suggestions on logistics operation in Sinotrans Guangdong warehouse & port for its future development.