The present invention provides a method of calibrating a position offset of a cursor on a screen such that, when a pointing device has already been moved to a position beyond the screen boundary, virtual coordinates of the pointing device are calculated and recorded to track the physical positions of the pointing device efficiently, and then the position offset between the pointing device and the cursor on the screen is compensated and corrected, so as for the user to greatly reduce the hassle of manually operating the pointing device for controlling cursor movement and thereby operate the cursor on the screen at will.