The invention relates to a method for manufacturing an LED chip substrate structure, comprising the following steps: plating a layer of metal layer on the surface of a sapphire substrate, forming a layer of photoresist film layer on the metal layer, patterning the photoresist film layer using the photoetching technology to form the desirable patterns, melting the photoresist film layer using the reflux technology to form a plurality of convex hulls; and transmiting the profiles of the convex hulls on the substrate using the inductively coupled plasma etching process to form convex-hull microstructures on the substrate. By plating a layer of metal on the substrate, the influence from the bond energy of the sapphire substrate to the photoresist can be isolated, therefore, the photoresist iscapable of refluxing more ideal patterns on the surface of the metal layer to help make good-quality substrates with microstructural patterns, reduce the internal absorption and boundary reflection of the LED chips, improve the defect of epitaxial growth, and increase the luminous efficiency of chips.