In this paper, a disturbance observer based control (DOBC) framework is proposed to achieve the motion control of an underwater biomimetic vehicle-manipulator system (UBVMS) driven by bionic flippers with mismatched disturbances. First, a disturbance observer is established to estimate the mismatched disturbances in finite time. Then, a novel arctangent non-singularity sliding mode manifold incorporating the disturbance observer is proposed to counteract the lumped mismatched disturbances. The stability of the system is validated by the Lyapunov theory. Finally, various comparative simulations are carried out to validate the performance of our proposed DOBC framework in the presence of mismatched disturbances.