A light-emitting diode substrate, a manufacturing method thereof, and a display device are disclosed. The manufacturing method of the light-emitting diode substrate includes: forming an epitaxial layer group of M light-emitting diode chips on a substrate; transferring N epitaxial layer groups on N substrates onto a transition carrier substrate, the N epitaxial layer groups on the N substrates being densely arranged on the transition carrier substrate; and transferring at least part of N*M light-emitting diode chips corresponding to the N epitaxial layer groups on the transition carrier substrate onto a driving substrate, an area of the transition carrier substrate is greater than or equal to a sum of areas of the N substrates, M is a positive integer greater than or equal to 2, and N is a positive integer greater than or equal to 2.