The water-rich zones in the coal fields of Northern China have seriously threatened the safe production of coal mines. It is necessary to accurately locate the deep seated and complex water bodies which are usually located in Ordovician limestone. Due to the relatively high cost of seismic exploration, the development effective electromagnetic detection methods and corresponding data processing techniques for the detection of these water-rich areas becomes a topic for the EM geophysicist. In this study, a method of rapidly estimating the burial depth and undulating morphology of coal bed foundations by employing frequency domain electromagnetic sounding data was proposed. The method uses the overshoot/undershoot phenomenon of the apparent resistivity for the frequency domain electromagnetic measurement to quantitatively determine the burial depth of the northern China coal structure bases. First, the featured frequency points were confirmed, where the overshoot and undershoot effects appeared in the electromagnetic sounding curves beside the borehole drilling sites. Then, the correlation coefficient between the confirmed frequency points and the burial depth of coal seam bed was obtained according to the drilling data. Finally, the burial depth of the coal seam beds in the entire survey area was evaluated based on the correlation coefficient and electromagnetic data. This method was applied in the northern areas of Taiyuan City in Shanxi Province, and achieved good results.