A real-time correction method based on Global Navigation Satellite System difference is proposed for the atmospheric phase disturbance of the antenna array. The atomic clock with high stability is used as the external frequency standard, the single difference of the carrier phase and the double difference on the epoch between the two stations are utilized, and the phase change caused by the satellite movement is deducted through the ephemeris. After the cycle slip detection and correction, the satellite orbit and the coordinate error of the station are eliminated through the long period fitting. Finally, the real-time measurement of ionospheric and tropospheric disturbances in two places is realized by dual frequency or multi frequency signals. A set of Global Navigation Satellite System receiving equipment was deployed at Miyun Observing Station and Kunming Observing Station of the National Astronomical Observatory of the Chinese Academy of Sciences, to verify the real-time correction method of atmospheric phase disturbance. The results show that the root-mean-square of the corrected atmospheric phase disturbance reaches 1.9 mm, modified by using the dual frequency carrier phase, under different weather conditions. The results indicate that the method can be used for the correction of the atmospheric phase disturbance of the antenna array in radio astronomy and deep space exploration.