The present invention relates to a device for controlling removal efficiency of nitrogen oxide in an SCR system, capable of selectively changing removal efficiency of nitrogen oxide (NO_x_) of an SCR system and improving economic feasibility of operation of a vessel by supplying a reducing agent in accordance with the selected removal efficiency of the nitrogen oxide. According to the present invention, the device for controlling removal efficiency of nitrogen oxide in an SCR system comprises: an SCR reactor providing a space in which reduction reaction of the nitrogen oxide in exhaust gas and the reducing agent proceeds; a reducing agent supply device supplying the reducing agent to the SCR reactor; a GPS calculating the position of the vessel in real time by receiving a signal which a GPS satellite sends; and a control unit storing multiple pieces of information about the removal efficiency of the nitrogen oxide and storing information on a supply amount of the reducing agent in accordance with the each removal efficiency of the nitrogen oxide, wherein the control unit also stores the information on the removal efficiency of the nitrogen oxide in accordance with the position of the vessel. The control unit selects the predetermined removal efficiency of the nitrogen oxide based on the position information on the vessel confirmed by the GPS and controls the reducing agent supply device in order for the predetermined amount of the reducing agent to be supplied to the SCR reactor based on the information on the supply amount of the reducing agent in accordance with the removal efficiency of the nitrogen oxide.
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