Abstract: Flexible structures actuated by smart materials have been widely used in the fields of underwater bionic robotics, precision medical machines, micro/nano devices, and so on. It is still a challenging task to acquire the hydrodynamic force exerted on the oscillating flexible structure by the surrounding fluid. The fluid-structure coupled dynamic equation of the MFC-actuated flexible structure is established. A cantilever-based measurement system for the hydrodynamic force is proposed, and the performance indexes are also proposed. The characteristic parameters of the force measurement device are calibrated by experiments. Then, dynamic variations of the hydrodynamic forces exerted on the MFC-actuated flexible structure at different actuation levels are acquired using the proposed system. The measured hydrodynamic forces are decomposed into two components, namely, the added mass force and the hydrodynamic damping force. Moreover, the inertia and drag coefficients in the form of Morrison’s expression are obtained. Experimental results show that the underwater oscillating amplitude of the MFC-actuated structure increases from 3.67 mm to a maximum of 4.23 mm, as the excitation frequencies increase from 2.5 Hz to the resonant frequency of 3.1 Hz. Accordingly, the measured hydrodynamic force exerted on the oscillating structure increases significantly from 86.16 to 184.83 mN. However, the hydrodynamic force stays roughly unchanged, differing by no more than 15%. The proposed method and measurement system may be helpful for the design and application of the underwater flexible structure actuated by MFC and other smart materials.