As an important guarantee for the construction of Hainan Free Trade Port，the roll-on/roll-off（Ro-Ro）transport of passenger and freight in Qiongzhou Strait bears more than 90% of materials for production and life and over 30% of the passengers entering and leaving Hainan Island，which is a major channel for people’s livelihood linking Hainan Province and inland areas. With the function adjustment of Xiuying Port of Haikou Port and the upcoming construction agenda of the Zhanjiang-Haikou high-speed railway project，the Xinhai Port of Haikou Port will be the core Ro-Ro port area on Hainan Island for Ro-Ro transport of passenger and freight and railway ferry on the whole island. Considering the existing problems in the Xinhai Port water area，we carry out the water area layout according to future development needs and simulate the water layout and the impact of channel navigation. The simulation results verify the rationality of the proposed water layout，which can ensure the navigation safety of Qiongzhou Strait.