This paper proposes a wireless control system for a 3D Microscope which is designed to move in two directions - polar and azimuth angle. Both angles are controlled with electric motors based on the users joystick command and the pechan prism motor is controlled to compensate image rotation whiling moving in polar angle. Since 3D microscope can be used for arbitrary rotation in azimuth angle, wireless control system is proposed to avoid twisting of power and signal wires. The validity of our system is shown through experimental works.