To improve positioning accuracy of a magnetic head in hard disk drives (HDDs), a triple-stage-actuator system was proposed with a thermal positioning actuator for a magnetic head positioning system. This positioning system has three types of actuators: a voice coil motor (VCM), piezoelectric (PZT) actuators, and the thermal positioning actuator. In this system, a magnetic head has a heater located in a horizontal direction of read/write elements as the thermal positioning actuator. By using this structure, the control system can move the position of read/write elements of the magnetic head in a horizontal direction with thermal expansion induced by the heater with an electric current. The thermal actuator systems have simple characteristics without mechanical resonant modes even in a high frequency range. This means that the thermal actuator is good for positioning control in high frequency range. As a result, the triple-stage-actuator system enable us to improve the positioning accuracy during a trackfollowing control from conventional dual-stage-actuator systems. However, the thermal positioning actuator causes flying height fluctuations of the magnetic head that could lead to fall of magnetic recording performances. In HDDs, the magnetic head has another heater located in a vertical direction of read/write elements in order to control flying height of the read/write elements. This control system is called thermal flying height control system. In the previous study, we can compensate for the flying-height fluctuations by using a feedforward control scheme of the TFC system. However, the feedforward control has little robustness against the plant perturbations. To address this issue, this paper employs a two-degree-of-freedom (TDOF) control scheme for the coordinated control with the TPC and the TFC systems. By using proposed TDOF method, we can compensate for the flying-height fluctuations against the plant perturbations. Simulation results showed that the proposed method is able to improve robust performance against the plant perturbations.