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