According to the requirements of regional control of coal seam floor water disaster in Zhaogu No.2 Mine, the thin layer L8 limestone at the bottom of Taiyuan Formation was selected as the target layer to carry out bedding drilling grouting to accurately explore and control the water conducting channel. However, the thickness of the target limestone layer was only 4 ~ 6 m, the local structural changes were complex, the characteristics of the roof and floor mudstone were similar and difficult to distinguish, and the instrument of measurement while drilling had hysteresis and other factors, bringing about that the drilling trajectory was easy to deviate from the target layer. And after drilling away from the target layer, sticking occurs in mudstone, which caused that the construction risk was high, the efficiency was low and the cost was increased. In order to improve this problem, based on the engineering practice of Zhaogu No.2 Mine, this paper proposed a set of thin-layer limestone bedding drilling technology system integrating geological identification and trajectory control.The contents included : ① The geological-directional integrated control mechanism was established to realize the sharing and dynamic analysis of cuttings, drilling time, hydrochloric acid reaction rate, gamma while drilling, trajectory parameters, and construct and iteratively update the geological model. ②Segmentation method was used to optimize the trajectory design of horizontal section, and the range of hole inclination angle was set with the formation dip angle as the constraint. ③Fusion of ' cuttings-drilling time-hydrochloric acid experiment-gamma ' quaternary comprehensive layering technology, real-time and accurate identification of lithology and bit position. ④Aimed at the intraformational flint strip marker layer, the ' wave ' interlayer tracking drilling control strategy was implemented, and the marker layer was used as the reference point to dynamically adjust the trajectory and continuously correct the model. The field practice in Zhaogu No.2 Mine showed that the technical system significantly reduced the risk of out-layering in the process of thin-layer limestone bedding drilling, improved the drilling efficiency and safety, and provided reliable technical support for the regional control project of coal seam floor water disaster.