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This paper is devoted to the control design and implementation of the dual-stage actuation system with a newly developed microthermal actuator (MTA) as the secondary actuator. The characterization and modeling of this new MTA is presented for controller design. Its performances such as stroke, time constant, and a good linearity are exhibited. The controller design of the MTA-based dual-stage actuation system is then proposed, and aims to push the bandwidth with the MTA. The simulation and the experimental testing have demonstrated the achievable 6-kHz bandwidth with 60-kHz sampling rate, the MTA displacement of 15 nm at 4 kHz, and 0.1-ms seeking time for 40-nm seeking length.