In order to precisely control the operations such as floating transportation,sinking, docking and buttjointing in the underwater construction of inland river immersed tunnel,the marine navigation system is introduced and successfully applied to the immersed pipe construction of Honggu Tunnel. Through analyzing the working principle and measuring method of the system, it is concluded that the system can meet the construction requirements of floating, sinkingand jointing of pipe joints in this project in terms of measuring and positioning accuracy.Combined with the realtime monitoring system, a precise control system for the above processesis formed.The controlled operation flow of the system is demonstrated through engineering example, which can provide valuable experience and implementation method for similar immersed tunnel projects.