A package substrate structure includes a first substrate, a second substrate, a plurality of conductive pillars and an adhesive layer. The first substrate includes a plurality of vias and a plurality of pads. The vias and the pads are disposed on the first substrate, and fills the vias. The second substrate is disposed opposite to the first substrate. Each conductive pillar is disposed between the first substrate and the second substrate, where each conductive pillar electrically connects each pad and the second substrate, and the adhesive layer fills the gaps between the conductive pillars. A bonding method of the package substrate structure is also provided.