Abstract: Stratigraphic sedimentation directly affects the development conditions of the underground aquifer,especially on the unconformity contact surface,the characteristics of the aquifer and aquiclude will be changed.Through the analysis of weathering zone and the paleo-bed characteristics of the unconformity surface of the stratum,then generalization of sedimentary laws and hydrogeological structures and hydrogeological exploration methods are used to study the structure of aquifers and aquifuges,it is proposed that the unconformity of the stratum easily causes the across stratigraphic boundary hydrogeological phenomena,that the stratigraphic boundary do not coincide with the hydrogeological boundary.It is expressed that the aquifer is forced to cross the stratigraphic boundary and develop in different strata.The different types of hydrogeological phenomena are analyzed,then three types of cross-layer hydrogeological structure models are generalized,namely “parallel-thinning” type,“parallel-thickening” type and “erosion-thickening” type.This paper analyzes the sedimentary geological and hydrogeological conditions of the main coal-producing areas in China,then studies the across stratigraphic boundariy hydrogeological phenomena and the formation conditions of Zhiluo Formation sandstone aquifer and the Ordovician limestone aquifer and their effects on mine water disasters in Jurassic coalfields in the Ordos Basin and Carboniferous-Permian coalfields in North China,and proposes comprehensive water prevention measures.The research indicates that the across stratigraphic boundary hydrogeological phenomena of Yan'an-Zhiluo Formation in Jurassic coalfield mining make the thickness of the aquiclude is reduced,so hydrogeological conditions more complicated.The hydrogeological phenomenon of the top of the Ordovician limestone in the Carboniferous-Permian coalfield increases the thickness of the aquiclude,so part of Ordovician limestone layer can be used as aquiclude,which contributes to the prevention and control of water disasters from coal seam floor.