A hybrid structure of multi-layer substrates comprises a first multi-layer substrate and a second multi-layer substrate. The first multi-layer substrate stacks up first metal layers, first dielectric layers alternately and has VIAs. A border district of a first metal layer connects with a border district of the corresponding first dielectric layer. The border districts are separated from adjacent first metal layers and adjacent first dielectric layers. The second multi-layer substrate stacks up second metal layers and second dielectric layers alternately. A border district of a second metal layer connects with a border district of the corresponding second dielectric layer. The border districts are separated from adjacent second metal layers and adjacent second dielectric layers. The VIAs are located at the border districts of the first dielectric layers and each VIA has electric conductor therein to connect one first metal layer with one second metal layer.