This study presents a co-simulation framework that integrates MATLAB/Simulink with the UUV Simulator to enhance the validation of trajectory tracking control strategies for underwater vehicles. Centered on the RexROV platform, the framework synchronizes high-fidelity hydrodynamic modeling with real-time control logic implementation. A cascaded PID architecture employing dual-loop position and velocity regulation is systematically compared with a conventional single-loop position controller across various operational scenarios, including station-keeping, linear trajectory tracking, and spiral path following. Results indicate that the cascaded controller offers superior handling of nonlinear dynamics and coupled motions, yielding significantly improved steady-state performance. The core innovation of this framework lies in its physics-informed simulation environment, which rigorously incorporates hydrodynamic effects. By bridging theoretical control design with practical implementation, the proposed methodology offers a credible and synchronized validation platform. While not aiming to replace modern nonlinear or adaptive techniques, this framework emphasizes practical advantages such as ease of tuning, low computational cost, and compatibility with industrial deployment. It enhances environmental realism beyond that of traditional single-tool simulations while remaining compatible with rapid prototyping workflows, thereby providing researchers with a standardized yet flexible testbed for evaluating underwater control systems in ecologically representative conditions.