The objective of this study is to suppress the relative displacement between lens set and granite platform using a micro flexible positioning mechanism, installed between lens set and gantry, with active vibration control. The relative displacement between lens set and granite platform was measured by a sensor and was then sent to a controller as input. If there is any horizontally relative displacement, the controller will send an output signal to a piezoelectric actuator in the positioning mechanism to cancel out the relative displacement. In the current study, a PID controller was applied to control the single axis mechanism. The displacement signal was detected by a laser displacement transducer for the feedback control. In addition, a mathematical model is set up for the piezoelectric micro positioning stage to simulate the performance of the PID controller under step inputs. Output displacement responses of the flexible positioning stage are observed by varying the proportional, integral, derivative parameters of the controller. The goal of this study is to suppress the horizontally relative displacement of 15 ∼ 20μm(peak value) between the lens set and granite platform under a frequency range of 0 ∼ 10 Hz. Through simulations and experiments of dynamic tracking, it was verified that the vibration of stage is effectively decreased to 2 ∼ 3μm after control under the proposed frequency range.