The invention discloses a two-dimensional scanning method for a biological chip scanner. The two-dimensional scanning method comprises the steps that a biological chip on a scanning platform moves outside a scanning region, a Y-direction motor intermittently steps on a Y-axis direction, the biological chip steps from a Y axis to a first scanning line starting point, and the Y-direction motor is stopped; the scanning platform is driven by an X-axis motor to move in an X-axis direction into the scanning region, when a first scanning line of the biological chip is scanned and crosses a boundary, the Y-direction motor and the X-direction motor are started to simultaneously move; g the Y-direction moves along the Y-axis direction, the biological chip moves to a starting point of a second scanning line on the boundary along a curve, and the Y-direction motor is stopped; the scanning platform is driven to a secondary scanning boundary by the X-direction motor, the scanning platform negatively moves into the scanning region from the starting point of the second scanning line along an X axis, when the second scanning line of the biological chip is scanned and crosses the first scanning boundary, the Y-direction motor is started to move along the Y-axis direction, and when the Y-direction motor moves to a third scanning line, the biological chip is stopped moving in the Y-axis direction; an nth scanning line is circularly scanned until reaching an end point.