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The dual-stage actuation system based on a newly developed slider-level thermal microactuator has been demonstrated to be able to achieve 6 kHz control bandwidth with 60 kHz sampling rate. This paper reports the saturation control for the thermal microactuator. The aim is to release the thermal microactuator from saturation as soon as possible once the saturation occurs, and to maintain the system to be stable when the microactuator saturates. Typically, the antiwindup compensation scheme is used, due to its benefits of easy design and implementation as well as effectiveness for the thermal microactuator. Simulation and experimental testing shows the performance of this saturation control, when the dual-stage system undertakes a seeking task, especially a long distance seeking such as 40 and 80 nm seekings.