Under the condition of complex structure and superimposed distribution of multi-layer limestone, thin-layer limestone had the characteristics of small thickness, unobvious horizon mark and easy to be confused with adjacent rock strata. When surface directional drilling was used for water disaster control, it was difficult to identify the horizon and the misjudgment rate was high, which directly affected the control accuracy and engineering safety. In order to solve this problem, based on the regional control project of thin limestone in Liangbei No.2 well, the problems existing in the original method of judging layer under complex geological conditions were analyzed. The judging layer index was optimized from the aspects of lithological characteristics, geophysical response and structural correction. The three-in-one comprehensive judging layer technology of " lithology identification + geophysical identification + structural correction " was constructed, and a standardized layering process was formed. The field application results showed that the optimized judgment layer technology could significantly improve the identification accuracy of thin limestone and the one-time hit rate of target layer, reduce the construction deviation and rework rate, and improve the control effect and construction efficiency. The research results could provide reference for directional drilling layer judgment and regional control projects under the conditions of complex structures, multiple limestones and thin layers.