Provided are a multi-layer interconnection structure and a manufacturing method thereof. The multi-layer interconnection structure includes a substrate; a first wiring on the substrate; an interlayer insulation layer on the first wiring; a second wiring on the interlayer insulation layer; and a via contact including at least one conductive filament penetrating through the interlayer insulation layer between the second wiring and the first wiring to be electrically connected to the first wiring and the second wiring.