An apparatus for controlling the Z axis position of a wafer prober includes a first sensor unit including a plurality of pressure sensors distributed and installed between a Z axis support plate, for supporting a Z axis transferring unit and a Z axis base. Actuators are distributed and installed between the Z axis support plate and the Z axis base, and lift up or lower the Z axis support plate. A driving unit drives the actuators. A control module controls the driving unit to drive the actuators in response to pieces of sensed data. The control module drives the actuators when a difference between the pieces of sensed data is greater than a preset difference limit value, thus enabling the chuck plate to be maintained in a horizontal state.