A structure of a packaging substrate having capacitors embedded therein is disclosed. The structure comprises a core substrate, a dielectric layer, and an outer circuit layer. The core substrate comprises an inner circuit layer. The dielectric layer is disposed at both sides of the core substrate, having first conductive vias each connecting to the inner circuit layer through a piece of outer electrode plate, a piece of high dielectric material layer, a piece of inner electrode plate, and a piece of adhesive layer, in sequence. The outer circuit layer is disposed on the surface of each of the dielectric layers. Herein, the capacitor is composed of a piece of the outer electrode plate, the high dielectric material layer and the inner electrode plate. The invention further comprises a method for manufacturing the same. This can achieve low costs, avoid the formation of voids, and reduce parasitic capacitance.