A package structure is provided. The package structure includes a first under bump metallurgy (UBM) layer formed over a first substrate, a first protrusion structure formed over the first UBM layer, wherein the first protrusion structure extends upward away from the first UBM layer. The package structure includes a first electrical connector formed over the first protrusion structure. The first electrical connector is surrounded by the first protrusion structure, and the first protrusion structure has an outer sidewall surface, and the outer sidewall surface of the first protrusion structure is aligned with an outer surface of the first UBM layer.