System configuration capacity and the structure of comprehensive transportation corridors vary due to the differences in natural condition, social economic level, and location within its network and its own utilities. This paper brings up a two-step method of highway facility structural allocation based on analysis of influence factors of facility allocation within a comprehensive transportation corridor. First, build a modified incremental Logit model, do a mode split and confirm the traffic flow on each link per kilometer by twice route distribution. Then, construct an evaluation system using the Analytical Hierarchy Process (AHP) to filter the feasible plans in order to pick out the optimal plan which could satisfy not only the transport need, but also could coordinate development with other transportation modes. Last, conduct road infrastructure optimization in the eastern transport corridor of Hainan as a case study. The development of a city is separated into several stages: (1) the infancy stage, powered by human or natural forces; (2) the developing stage, stimulated by canal and railway transport; and (3) the mature stage, based on integrated transport methods. Each transport mode differs from others, leading to the competitive and cooperative relations between those modes. From a system optimization point of view, Dong Kun (Dong Kun, 2010) and Si Bingfeng (Si Bingfeng, 2005) cast research on the corridor structural optimization for relatively stationary origin destination (OD) points, which solved the coordination and optimization problem for the competitive relationships in the corridor. Yet, the drawback is the lack of analysis of needs and supply, only feasible for very limited cases. Therefore, this paper allocated highway facilities in the corridor for each stage by taking consideration of each mode's supply characteristics regarding the corresponding stage's transport needs, respectively, based on the system planning points of view (Wang Jianwei, 2004).