Through practical application, theoretical deduction and simulation calculation, the validity of the frequency selection method of natural electric field in shallow groundwater exploration was illustrated, and the natural field source component which plays a major role in the formation of anomaly was analyzed. The method had been applied to 12th Five-Year Plan of the rural drinking water safety project by No. 273 Geological Party of Guangxi in 2013~2015. According to its exploration results, a total of 131 wells were drilled. 114 wells' water output was more than 1m ³/h, accounting for about 87.0% of the total amount of drill holes. The practical application shows that the frequency selection method is practical and feasible in shallow groundwater exploration. On the basis of practical application and previous research results, a spherical water filled karst model in uniform half space was designed, and the magnitude of the secondary electric field on the main section of the surface was calculated by using analytic method. The calculated results show that the horizontal alternating magnetic field produces a relatively high potential anomaly, whereas the horizontal alternating electric field produces a relatively low potential anomaly. It can be concluded that the formation of anomaly of frequency selection method in groundwater exploration is mainly due to the effect of alternating electric field components.