A substrate processing apparatus and a lift pin alignment apparatus, the substrate processing apparatus including a chamber; a substrate plate on which the substrate is seatable; a plurality of movable lift in the substrate plate to support the substrate; a leveling sensor configured to be loadable in the chamber on the lift pins; a controller configured to receive measurement values of roll (φ) and pitch (θ) of a plane of the lift pins to calculate a rotation matrix (T) of the plane from the measurement values of roll (φ) and pitch (θ), and to calculate travel distances of the lift pins for leveling the plane to be parallel with a horizontal reference plane by using the rotation matrix (T) and to output a lift pin control signal for aligning the lift pins; and a lift pin driver to move the lift pins according to the lift pin control signal.