This paper presents a novel beam flexure-based X-Y-θ micro-stage integrated with a laser interferometric type displacement measurement approach for reducing the measurement error induced by the rotational motion and cross-axis load effect. Aiming at achieving high-precision real-time control of the proposed system, an active disturbance rejection controller is developed such that the inevitable parasitic and coupling errors can be treated as disturbances and actively compensated by using the extended state observer. Finally, the verification experiments are deployed on the fabricated prototype, where the results indicate that the proposed approach achieves excellent performance in terms of motion accuracy and disturbance rejections.