To realize high precision position control of a gene sequencer motion stage, a gene sequencer motion stage control system was developed, and its applied methods such as mathematical modeling, model identification, controller design, and input shaping were investigated. First, based on the dynamic equation of the motion stage and the voltage-force relationship of a permanent magnet linear synchronous motor, a model of the motion stage was established. Then the method of frequency domain scan was adopted to determine the model parameters. Finally, a compound controller, combined with a double closed loop controller and forward feedback controller, was designed based on the model of motion stage to ensure stability and high precision of the motion stage, and an input shaper was designed based on the dominant pole of the compound control system to eliminate oscillation in the motion stage. Experimental results indicate that the compound controller with the input shaping improves the repeated positioning accuracy of the motion stage from ±1.47 μm to ±0.354 μm. The proposed design allows the motion stage to achieve the ultimate repeated positioning accuracy faster than the conventional compound controller, and satisfies the requirements of high stability and precision when the gene sequencer generates an image.