Vibration noise has an influence on the sensitivity and stability for many precision instruments, especially for atom interferometers. In this paper, a mobile three-dimensional active vibration isolation system is established for portable atom interferometer that is effectively isolated from the ground vibration, thereby improving the sensitivity of the portable atom interferometer, and can be deployed and recovered to working state rapidly. With the home-developed integrated feedback algorithm, this system achieves a good vibration suppression in a wide frequency range in three directions. It suppresses the ground vibration by three orders of magnitude in the vertical direction, and one order of magnitude in the horizontal direction. In a frequency range less than 10 Hz which the atom interferometer is sensitive to, the vibration noise is suppressed to 4.8 × 10^–9 m/s²/Hz^1/2 in the vertical direction and to 2.7 × 10^–7 m/s²/Hz^1/2 in the horizontal direction. The influence of vibration noise on the sensitivity of the atom interferometer reaches to 2 μGal/Hz^1/2, which is reduced by two orders of magnitude compared with the result without our system.