This project demonstrated an Autonomous Underwater Vehicle (AUV) equipped with integrated sensor and depth controller based on the pressure sensing which able to continuously sending the depth data to controller. The project is to develop a depth controller for AUV to submerge accurately. The depth Simulink Arduino algorithm is implemented on an Arduino Mega using Model-Based Design (MBD) with MATLAB and Simulink. MBD used to model, simulate and verify the Simulink control algorithm after obtained data through open-loop experiment test. Then, it deploys and tests the algorithm on the embedded AUV hardware. The focus was in controlling the AUV vertical trajectory as the AUV tried to remain stationary at the desired depth and having its overshoot, rise time and settling time minimized. The comparative study for the AUV depth-control by On-Off, Proportional Integral Derivative (PID) and Fuzzy Logic Controller (FLC) controllers. MBD has faster implementation with fewer coding error when deploy to AUV hardware.