A wafer-level package structure of a light emitting diode and a manufacturing method thereof, and the package structure includes: a die including a first side and a second side opposite to the first side; a first insulating layer on the first side of the die; at least two wires which are arranged on the insulating layer and electrically isolated from each other; bumps which are arranged on the wires and adapted to be electrically connected correspondingly with electrodes of a bare chip of the light emitting diode; at least two discrete lead areas on the second side of the die; and leads in the lead areas, electrically isolated from each other and electrically connected correspondingly with the wires. The invention forms the leads on the second side of the substrate to extract the electrodes of the light emitting diode, that is, the light emitting diode and the leads thereof are located on the two opposite sides of the substrate in the technical solution of the invention, to thereby reduce the area required for the substrate; and the electrodes can be extracted in the subsequent structure of the package without gold wiring to thereby further reduce the volume of the package.