An optimization model of China railway freight station layout based on agent and human-element-model has been put forward to solve the problems that have hindered the normal product, such as too many railway freight stations and too clear distance between stations, and so on. The model uses the classical Sugars cape as the reference and integrates the intelligence of Agent and the combination of subjectivity and objectivity of Human-element. The owners are regarded as autonomic Agents and the freight stations are regarded as resources in the model. The Agent energy can change during it seeks the resources, and its value is decided by its own energy. According to the set rules, a freight station layout in a definite scope is obtained through stimulation analysis, and the existing processes of different owner are analyzed. The simulation results show that the model has the characteristics of intelligence and autonomy, and it is meaningful to optimize the freight station layout and set the strategic cargo-loading and logistics strategy.