Disclosed is a method of manufacturing a hybrid structure of multi-layer substrates. The method comprises steps of: separating a border district of at least one metal layer connecting with a border district of the corresponding dielectric layer from adjacent metal layers and adjacent dielectric layers for each multi-layer substrate and connecting a separated border of a metal layer of one multi-layer substrate with a separated border district of a metal layer of another multi-layer substrate to form a connection section. The hybrid structure comprises at least a first multi-layer substrate and a second multi-layer substrate. At least one first metal layer is connected with at least one second metal layer to form a connection section.