Water inrush from Ordovician karst aquifer in North China coal mine has become a key issue on underground coal mining. To address this problem, it is necessary to identify fault zones, because fault zones might connect limestone aquifers and coal seams, enabling Ordovician karst water to enter the mine. In the study area, a series of parallel directional holes were drilled along Ordovician limestone at depths between 70 and 90 m under Ordovician limestone boundary. To conveniently detect fault zones and govern mine water disasters, a series of natural gamma-ray logging while drilling (GRLWD) were undertaken. The entire detecting region can be comprehensively covered by several directional borehole groups. Then, fast Fourier transform and short-time Fourier transform approaches were employed on the basis of GRLWD data and geological data to extract faults information. A segmented identification method for deep fault zones was established in this study. This method can be used to markedly improve the identification of fault zones within Ordovician limestone or the unitary lithology formation and provide crucial information relevant for deep coal mining safety.