Abstract: Geological effect of karst water prospecting by natural electric field frequency selection method and the cause of anomaly formation were discussed in this paper. Eleven exploration lines of frequency selection method were designed in four areas appointed by Guxu coal mine. Distribution of water-filled karst was predicted in working area by data processing and result analysis and in combination with the local topographic and geologic conditions. The geophysical interpretation result is credible from the comparison of geophysical results with geological exploration data and tunnel excavation data. This geophysical method can be used to investigate groundwater, and it is the scientific basis for the design of roadway and drainage, prevention and control of water hazards. On the basis of practice and from Maxwell equations, the author deduced the formula of induced electric field of a horizontal cylinder in homogeneous harmonious electromagnetic field, and calculated electric field intensity. According to the comparison of the horizontal component of induced natural electric field with the experimental curve, anomalies of frequency selection method are caused by induced secondary field.