A layer structure with an electromagnetic interference (EMI) shielding effect is applicable for reducing an EMI effect caused by signal transmission between through silicon vias, so as to effectively provide the EMI shielding effect between electrical interconnections of a three-dimensional (3D) integrated circuit. By forming EMI-shielding through silicon vias at predetermined positions between the through silicon vias used for signal transmission, a good EMI shielding effect can be attended, and signal distortion possibly caused by the EMI effect can be reduced between different chips or substrates.