By patterning sapphire substrate (PSS) and then growing gallium nitride (GaN) film through wet etching process, the generation of dislocation and lattice defects of LED substrate can be significantly reduced, and the luminous efficiency and stability of the prepared led beads can be greatly improved. Due to the current anisotropic etching mechanism of sapphire has not been fully revealed, the etching evolution process and structure morphology cannot be accurately predicted and controlled, and ultimately it is difficult to ensure the structural quality of the patterned substrate. In this study, the etching rates of all crystal planes of sapphire in 98%H2SO4:85%H3PO4 = 3:1 etching solution were obtained through experiments, and the microstructure etching process and surface morphology were analyzed in detail. In addition, the influence of etching conditions on sapphire etching microstructure and surface morphology was also analyzed through experiments. The experimental results show that: 1) increasing the temperature can speed up the etching reaction, but it will make the surface quality worse; 2) Phosphoric acid as an etching buffer can improve the quality of etched structural planes; 3) The optimal etching rate and surface quality can be obtained by etching in 98%H2SO4:85%H3PO4 = 3:1 solution.