The invention discloses a method for manufacturing a three-dimensional through hole interconnection structure based on a molten glass skeleton, and relates to the interconnection technology of silicon through holes. Grooves are etched in a silicon layer, and silicon columns are formed. A screen printing plate with a pattern is made to align at the etched pattern of the silicon layer. Glass powder is arranged on the screen printing plate. The glass powder is extruded in the vertical direction to be filled into the grooves, and the screen printing plate is moved away. The glass powder on the surfaces of the tops of the silicon columns is removed. The silicon layer filled with the glass powder is heated and molten, no bubble exists inside the silicon layer, a molten glass structure is obtained after cooling, the silicon layer of the obtained molten glass structure is arranged in etching liquid, the remaining molten glass structure on the surfaces of the tops of the silicon columns is removed by the adoption of the wet etching technology, and the molten glass skeleton inside the grooves is obtained. By the adoption of the mechanical lapping mode, the lower portion of the silicon layer is machined in a thinned mode until the bottoms of the silicon columns are exposed out of the lower portion of the silicon layer, then, lapping damage is repaired by the adoption of the chemical mechanical polishing mode, and therefore the three-dimensional through hole interconnection structure based on the molten glass skeleton is obtained.