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Medical robotic system can extend surgeon's ability in minimally invasive surgery (MIS), which requires hand-eye coordination and dexterity of operation. According to surgical tasks, the control system of a novel robot is proposed. The modularized system is designed to meet the demands of various requirements in surgery, and the algorithm is established to realize the alignment between the master and the slave of the novel system. The preliminary motion control and the experiments verify the effectiveness of the designed control system.