It is essential for the diversity of operation targets during the underwater manipulator’s task. The joint friction, the time-varying characteristics of physical parameters, and inaccurate measurement of the dynamic bring trouble of model uncertainty. For these problems, a model reference adaptive impedance controller is proposed to achieve the manipulator flexible operation. The desired impedance model is designed for the outer loop force tracking, and the model reference adaptive impedance controller is employed for the inner loop. At the same time, the adaptive law is designed based on the operation space position and the desired position of the desired impedance model output. To eliminate the time-varying characteristics of physical parameters, a new bounded-gain-forgetting adaptive law is designed to compensate the uncertain error between the manipulator model and estimate model. It is ensured that the closed-loop manipulator dynamic is consistent with the desired impedance model, correspondingly the manipulator end operation force tracking the standard force signal is realized, and the desired position error of the end position of the manipulator to the desired impedance model output asymptotically converges to zero. The simulation experiment of a two-degree-of-freedom manipulator is implemented on the Matlab/Simulink platform. The results show that the designed controller has good force–position tracking asymptotical convergence ability under the uncertain dynamic, and the controller has robustness and stability performance.