A light-emitting device and a manufacturing method thereof are provided. The light-emitting device includes a substrate, an epitaxial blocking layer, and a light-emitting epitaxial structure. The substrate has a surface, in which the surface includes a plurality of protruding parts and a plurality of recess parts relative to the protruding parts. The epitaxial blocking layer disposed on the substrate covers the recess parts and exposes the protruding parts. The light-emitting epitaxial structure disposed on the substrate is connected to the protruding parts and is disposed above the recess parts. The light-emitting epitaxial structure is formed by using the protruding parts as a growth surface thereof so as to have a better crystalline quality.