Comparison is conducted between automatic soil moisture monitoring data and manual measured relative soil moisture data from the Meteorological Data Storage System (MDSS) of the National Meteorological Information Center (NMIC), and it is found that there is about 15% of difference between different observing times in daytime. According to the structural characteristics of the two sets of measurements and the operational requirements of the Chinese Meteorological Administration (CMA), the reasons for the differences are analyzed from several aspects, such as measurement and calculation, repeatable errors, differences in monitoring soil depth and monitoring time, calculation of soil moisture constant, and soil structure change, etc. It is concluded that when the various differences are overlaid together, the maximum difference of about 20% can be found; other factors are also known to impact the difference, so a difference of about 15% is reasonable in practice. The differences of the measured data between observing sites are analyzed by selecting a long sequence observation data. According to commonly used operational indicators of moisture level, the data disturbance and data loss influencing objective judgment induced by the data differences between the two methods are analyzed. It is suggested that the volumetric water content should be used directly in operational application analysis; new application methods of automatic soil moisture monitoring data should be developed, and the corresponding indicator systems or models should be established; the advantages of automatic soil moisture monitoring should be fully taken.