Inertial reference and positioning based on measurement and processing of acceleration data is needed for guidance and function controls of Autonomous Underwater Vehicles (AUVs). This work proposes a method to implements a low cost inertial navigation and positioning for remote monitoring system. The simulation presented involved of AUV receiving a simulated command to following at a particular trajectories. In practice, it be able to receive a command to certain trajectories at any time during her mission. This system can conduct the digital signals acquisition and processing which are output from the GPS receiver and micro inertial measurement unit, and the data is sent to the ground station in the form of messages periodically. Experiment results shows that the system hardware and software coordinate well and tightly coupled navigation system has a better accuracy and stability under high dynamic.