A method for forming the package structure is provided. The method includes forming a die structure over a first surface of a first substrate, and forming a plurality of electrical connectors below a second surface of the first substrate. The method also includes forming a first protruding structure below the second surface of the first substrate, and the electrical connectors are surrounded by the first protruding structure. The method further includes forming a second protruding structure over a second substrate, and bonding the first substrate to the second substrate. The electrical connectors are surrounded by the second protruding structure, and the first protruding structure does not overlap with the second protruding structure.