Abstract: By using precise point positioning with GNSS single station receiver, a method of estimating atmospheric structure constant C_n is introduced based on the time correlation of troposphere zenith delay and atmospheric refractive index which using classical Kolmogorov—Obukhov"2/3" turbulence theory and random field theory, and the atmospheric phase errors of two-element antenna array in different turbulence intensity environment are analyzed. The influence of atmospheric scattering on antenna array system is estimated by computing C_n² in four very long baseline interferometry(VLBI) deep space stations in China. The statistic results show that except on January in Beijing and Urumchi, the atmospheric phase errors in four stations are almost over 25°, and even more than 50° on July in Beijing and on April in Shanghai at Ka frequency, which would reduce SNR combining performance of antenna array seriously and affect the large capability communication between earth station and deep space detector.