A real-time controlling system used for controlling an intelligent active vibration isolation unit comprises an intelligent active vibration isolation unit, a base, a DSP vibration controlling card, a piezo-electricity type accelerating sensor, a signal collecting device and a signal conditioning device, wherein, the intelligent active vibration isolation unit is fixed on the base; when the base is vibrated, the signal collecting device collects two error signals and one vibration source signal on the horizontal and vertical planes of the intelligent active vibration isolation unit transmitted from the vibration source detected by the piezo-electricity type accelerating sensor, and all the three signals enter the DSP vibration controlling card; after the three signals are calculated through the control algorithm in the DSP vibration controlling card, two signals to be controlled are outputted and processed through the signal conditioning device, and the two signals to be controlled are outputted to two giant magnetostrictive actuators in the intelligent active vibration isolation unit in the horizontal direction and in the vertical direction, thereby generating relevant extension and shrinkage and realizing the active vibration control of the intelligent active vibration isolation unit. The invention has the advantages of quick speed, real time and high precision.