A multi-layer system-on-chip (SoC) module structure is provided. The multi-layer SoC module structure includes at least two circuit board module layers and at least one connector module layer. Each connector module layer is sandwiched between and thus electrically connects two circuit board module layers such that the SoC module structure is formed by stacking. Each circuit board module layer is composed of at least one circuit board module while each connector module layer is composed of at least one connector module. Hence, the SoC module structure can be manufactured as a three-dimensional structure, thus allowing highly flexible connections within the SoC module structure.