An anti-diffusion substrate structure includes a substrate, a substrate circuit layer, and a chip. The substrate has multiple through holes. Within each of the through holes includes a first metal layer and an anti-diffusion layer plated on the first metal layer. The anti-diffusion layer is an Electroless Palladium Immersion Gold (EPIG) layer or an Electroless Nickel Electroless Palladium Immersion Gold (ENEPIG) layer. The substrate circuit layer is mounted on the substrate and extended on the anti-diffusion layer within each of the through holes. The substrate circuit layer is made of a second metal layer, and a composition of the second metal layer is different from a composition of the first metal layer. The chip is electrically connected to the substrate circuit layer. The anti-diffusion layer is able to better prevent material of the first metal layer from migrating or diffusing to the second metal layer.