Disclosed are a multi-layer substrate and a manufacturing method of the multi-layer substrate. By employing a carrier to alternately form dielectric layers and metal structure layers thereon. Each dielectric layer adheres with the adjacent dielectric layer to embed the metal structure layers in the dielectric layers corresponding thereto. Comparing with prior arts, which have to use prepregs when hot pressing and adhering different layers of different materials, the present invention takes fewer processes, thus, fewer kinds of materials without using prepregs. Therefore, the present invention can promote the entire quality and yield of manufacturing the multi-layer substrate to satisfy mechanical characteristic matching of the multi-layer substrate and to reduce cost of the whole manufacturing process. Significantly, the multi-layer substrate having thin dielectric layers according to the present invention can satisfy the concern of impedance matching therefore, and can reduce crosstalk influence to keep good signal integrity therein.