The paper studies this global output regulation of a class of two order Port-Controlled Hamiltonian Systems with mismatched disturbance by a composite control method. By combining the damping injection, the finite time disturbance observer (FTDO) and the coordinate transformation techniques together, the composite controller is developed. The novel idea is to design a coordinate transformation to address the mismatched disturbance estimation. By the Lyapunov function method, the system output asymptotically converges to zero in the presence of mismatched disturbance. An example of a permanent magnet synchronous motor with simulations shows the effectiveness of the method proposed.