The invention discloses a method for manufacturing vertically interconnected substrates based on laser nano-processing technology. Firstly, a first circuit wiring layer is formed on one side of the substrate through photolithography, corrosion, and glue removal of the dielectric layer, and then the laser nano-processing technology is used to form the first circuit wiring layer on one side of the substrate. Blind holes are opened at the corresponding positions on the substrate, and then the substrate is placed in the electrodeposition solution for electrodeposition to fill the blind holes, and finally the second circuit is formed on the other side of the substrate through photolithography, corrosion, and degumming of the dielectric layer Wiring layer, the manufacturing method has a simple process, high precision of laser nano-processing technology, no void inside the through hole, reliable interconnection, and improves the density and reliability of the three-dimensional packaging of the LCP flexible substrate. At the same time, the metallized through hole is used to realize the double The vertical interconnection between the surface circuit wiring layers can effectively shorten the interconnection distance, reduce signal delay, reduce parasitic inductance and capacitance, improve high-frequency characteristics, and thus improve system integration performance.