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In order to estimate soil water content by ground-penetrating radar, an experimental was conducted at Fukang Station of Desert Ecology of Chinese Academy of Science located in the southern part of Gurbantunggut desert. Ground Penetrating Radar is used as the main data collection tool. Considering the higher accuracy of wide angle reflection refraction measurement and the faster speed of the fixed offset measurement of ground penetrating radar, a method is presented for the determination of optimal fixed offset based on the obtained average dielectric permittivity of the former. The result showed that: A decreasing trend for the average dielectric permittivity was found with increasing fixed offset of antennas Between 0.36-1.36m along survey line by fixed offset measurement. According to the minimum deviating principle of the average dielectric permittivity, 1.71 m was determined as the optimal fixed offset in the study, the ground wave of this fixed offset was picked and soil water content was calculated, and the average water content of 0.36-1.36 m along survey line is only higher 0.0016 m(3)/m(3) than that of wide angle reflection refraction measurements, the accuracy can meet the actual demand, the average water content of the upper sandy showed spatial heterogeneity between 0-36.5 m along survey line, This method can accurately fast estimate mesoscale soil water content which can provide a scientific basis for agricultural production and crop irrigation. (C) 2011 Published by Elsevier Ltd. Selection and/or peer-review under responsibility of the Organizers of 2011 International Conference on Energy and Environmental Science.