This paper introduces an innovative teaching approach for the nonlinear systems and intelligent control course, leveraging underwater flexible manipulator to enhance both theoretical comprehension and practical application. The proposed approach integrates fundamental knowledge of mechanical systems with simulation experiments, providing master’s candidates with a comprehensive grasp of modeling, analysis, identification, nonlinear dynamics, and control. By utilizing an underwater flexible manipulator model, students gain a deeper insight into dynamic characteristics and vibration control, particularly regarding the interaction between fluid and the flexible structure, which produce unique dynamic phenomena. This novel teaching method, adaptable to both on-campus and online formats, incorporates modeling of fluid and manipulator dynamics, frequency and modal shape analyses, as well as time-domain and parameter variation simulations. Furthermore, this approach extends to physical experimental platforms such as PLCs and cranes. The paper details course assignments, tests, and an advanced study segment, offering a robust framework for engaging students in nonlinear systems analysis and control.