An electronic chalkboard system, a control method thereof, and a pointing device are provided. The electronic chalkboard system includes a plurality of display panels; a pointing device which calculates coordinate information about a touched position based on a reference signal generated on the display panels when touching a first panel among the display panels; and an image processor which generates a signal differently set with respect to each of the display panels on the display panels to determine the first panel among the display panels and displays an image corresponding to the coordinate information calculated by the pointing device on the first panel.