The difference of spatial structure of fault-controlled paleokarst system is the key factor restricting the efficient development of this kind of reservoir. Taking Shunbei1 fault zone as an example, based on the information of structural interpretation, reservoir prediction, drilling and production characteristics, according to the hierarchy of scale, this work expounds their genesis and characteristics from the points of faults zone segmentation, fault-controlled paleokarst segmentation, hydrocarbon charging and fracture-cavern connectivity, reproduces the distribution law and interrelationship of different bodies at each level by means of three-dimensional geological modeling, and discusses the direction of tackling key problems in the next step. The results show that the strike-slip faults have interactive segmentation along the strike, and the segmental difference forms a stratigraphic fragmentation body with different width. On the basis of fragmentation body, the different dissolution degree leads to the spatial segmentation of the fault -controlled karst. Affected by the drainage capacity of the fault, the charging variance is obvious along the strike. A variety of fracture-cavern configuration relations further aggravate the internal heterogeneity of the karst reservoir. The idea of hierarchical modeling of fault-controlled karst system gradually shows the heterogeneity between different bodies, but the coupling law between different bodies needs to be further explored. This study can be used as a reference for promoting the theoretical understanding of fault-controlled karst reservoir and guiding the practice of development.