The invention provides a light emitting diode and a manufacturing method thereof and a light emitting device. The light emitting diode comprises a first electrode, used for connecting the light emitting diode and the negative pole of a power supply, as well as a substrate and a light emitting diode core which are sequentially arranged on the first electrode, wherein a plurality of contact holes penetrating through the substrate are formed in the substrate, the upper aperture size of the contact hole is larger than the lower aperture size of the contact hole, and the contact holes are filled with electrode plugs used for connecting the first electrode and the light emitting diode core. The light emitting device applying the light emitting diode provided by the invention also comprises a base, and the light emitting diode is arranged on the base. The manufacturing method of the light emitting diode comprises the steps of sequentially forming the light emitting diode core and a second electrode on the substrate, patterning the back of the substrate and forming inverted trapezium-shaped contact holes exposing the light emitting diode core, as well as filling conductive materials into the inverted trapezium-shaped contact holes until the first electrode covered on the back of the substrate is formed. The invention has the advantages that the light emitting efficiency of the light emitting diode is improved and the manufacturing process is simpler.