A three-dimensional programmable interconnection system based on a multi-chip package includes: a programmable metal bump or pad at a bottom of the multi-chip package; a first programmable interconnect provided by an interposer of the multi-chip package; a second programmable interconnect provided by the interposer; and a switch provided by a first semiconductor chip of the multi-chip package, wherein the switch is configured to control connection between the first and second programmable interconnects, wherein the programmable metal bump or pad couples to a second semiconductor chip of the multi-chip package through the switch and the first and second programmable interconnects, wherein the first and second semiconductor chips are over the interposer.