The invention discloses a vertical interconnection substrate manufacturing method based on a laser nanometer processing technology. The method comprises the following steps of photoetching, corrodingand degumming a dielectric layer to form a first circuit wiring layer at one side of the substrate, then, forming a blind hole at the corresponding position of the substrate by adopting a laser nano machining technology, putting the substrate into an electro-deposition solution for electro-deposition, filling the blind hole, and finally photoetching, corroding and degumming the dielectric layer toform a second circuit wiring layer at the other side of the substrate. The manufacturing method is concise in process flow, and the laser nano-machining technology is high in precision. Cavities do not exist in the through holes, the interconnection is reliable, and the density and reliability of the three-dimensional packaging of a LCP flexible substrate are improved. Meanwhile, the vertical interconnection between LCP double-sided circuit wiring layers is achieved through the metallized through holes, the interconnection distance can be effectively shortened, the signal delay is reduced, the parasitic inductance and capacitance are reduced, and the high-frequency characteristic is improved, and therefore the system integration performance is improved.