The invention provides a tool for realizing the integrated packaging structure of the vertical interconnection of a micro-system and a manufacturing method thereof. The tool comprises a first substrate, a first positioning plate and a baffle plate. The first substrate is used for assembling an antenna plate assembly. The baffle plate is positioned on the first substrate and can be adjusted and fixed. The tool further comprises a second substrate used for assembling an intermediate-frequency plate and a radio-frequency plate assembly, a second positioning plate and a baffle plate positioned onthe second substrate and capable of being adjusted and fixed. By means of the above tool, the integrated assembly of the four layers of tile-type structures of a micro-system is realized. The tool ishigh in packaging precision, and the vertical interconnection of the micro-system can be realized.