The invention relates to a multi-level fusion three-dimensional system integrated structure, and the structure comprises a tube shell, wherein a plurality of pins are arranged on the bottom surface ofthe tube shell, n substrate modules which are sequentially stacked are arranged in the tube shell, convex points are arranged between the n substrate modules, and every two adjacent substrate modulesare separated through the corresponding convex point. A silicon adapter plate module is further arranged above the n substrate modules, and convex points are also arranged between the substrate modules and the silicon adapter plate module, and the substrate modules and the silicon adapter plate module are separated through the convex points. Compared with an existing single-layer TSV technology-based structure, the integrated structure of the multi-layer fused three-dimensional system has the advantages that excessive dependence on the process of the existing single-layer TSV technology-basedstructure is avoided, the three-dimensional integrated process method is simplified, the product yield is improved, and the cost is saved.