This study focuses on a piezo-actuated two-degrees-of-freedom (2-DOF) decoupled compliant micro-positioning stage driven by a novel compound bridge-type amplification mechanism embedded with Scott-Russell mechanism. According to the system identification, the transfer functions of two working directions are obtained. Both of the measured dynamic cross couplings between them are also lower than −40 dB, demonstrating that the single-input-single-output control strategy can be adopted reasonably. Based on the identified frequency response, a fractional order proportional-integral (FOPI) controller is designed for the 2-DOF compliant micro-positioning stage. Compared with the integer order proportional-integral (IOPI) controller using same parameters, the amplitude error of the FOPI controller is 2% lower than that of IOPI controller. Additionally, a fractional order zero phase error controller (FOZPETC) is designed by obtaining the inverse of the fractional order closed-loop system in a large frequency range. And the gain of the corrected control system is 1 in a wide frequency band to eliminate the phase error in the close-loop control system. Finally, using the compound control strategy of FOZPETC+FOPI, a series of trajectory tracking tests are carried out on the proposed novel 2-DOF compliant micro-positioning stage. All the experimental results prove that the designed controller can achieve good positioning and tracking performance of the micro-positioning stage, and confirm the effectiveness of the compound control strategy of FOZPETC+FOPI.