The invention discloses an LED packaging structure and packaging method thereof. The LED packaging structure comprises a square bracket, wherein an LED chip is arranged at the center of the bowl cup of the bracket; the electrodes of the LED chip are connected with the positive and negative electrodes of the bracket by golden lines; a step is arranged on the bowl cup wall of the bracket; glue filling holes are formed in the four corner of the step; each glue filling hole is communicated to the bottom of the bowl cup; a glass sheet is arranged on the step; one surface of the glass sheet is coated with fluorescent powder; the surface, coated with the fluorescent powder, of the glass sheet faces downwards. The LED packaging structure and the packaging method thereof can be used for not only solving a problem of a yellow ring of white light of an LED, but also solving a problem of luminance decay of the white light of the LED; silica gel is injected into the bowl cup of the bracket by the glue filling holes, the operation is convenient, and the fluorescent powder can not be concentrated near to the LED chip or the bottom of the bowl cup of the bracket, and therefore, the luminance decay of the LED chip, caused by long-time heating, is avoided, and from another point of view, the service life of the LED is prolonged.