Seismic 3D full-horizon tracking is a fundamental and crucial step in sequence analysis and reservoir modeling. Existing automatic full-horizon tracking approaches lack effective methods for representing the stratigraphic sequence relationships in seismic data. However, the inability to represent the stratigraphic sequence relationships fully and accurately makes it challenging to address discontinuous areas affected by faults and unconformities. To address this issue effectively, we propose a knowledge graph representing the stratigraphic sequence relationship, which enables the simultaneous extraction of all horizon surfaces once the stratigraphic distribution of the seismic data is obtained. In this method, horizon patches are generated, and the fault attribute is calculated, followed by the construction of an initial knowledge graph that characterizes the overall distribution of both horizon patches and faults. The initial knowledge graph comprises nodes and edges. Here, the nodes represent horizon patches, and their attributes cover the geographical location information of the patches and faults. Simultaneously, edges represent the relationship between horizon patches, including the stratigraphic sequence relationship, and their attributes illustrate the potential of connecting these patches. Furthermore, we developed a multi-layer knowledge graph based on the point set topology to fuse the nodes. This allows for continuous merging of horizon patches to obtain horizon surfaces across discontinuities with the constraints of fault attributes and stratigraphic sequence relationships in 3D space. Both synthetic and field examples demonstrated that the proposed method can effectively represent the stratigraphic sequence relationships and accurately track horizons dislocated in discontinuous areas with faults and unconformities.