A joint structure and a manufacturing method thereof are provided which can improve heat dissipation properties and which can inhibit damages. A joint structure includes: an insulating substrate and a heat dissipation substrate; a first silver particle layer that is joined to the insulating substrate and that includes a plurality of first silver nanoparticles which are joined; a second silver particle layer that is joined to the heat dissipation substrate and that includes a plurality of second silver nanoparticles which are joined; and a copper particle layer that interposes the first silver particle layer and the second silver particle layer, that is joined to the first silver particle layer and the second silver particle layer, and that includes a plurality of copper nanoparticles which are joined. A particle size of the copper nanoparticles is larger than particle size of both the first silver nanoparticles and the second silver nanoparticles.