An analysis to model the thermoelectric (TE) effects of the rough InN/GaN core-shell nanowires (NWs) with wire diameter ranging from 25 nm to 100 nm is proposed. The elastic continuum model is employed to calculate the phonon dispersion relation curves and the related phonon group velocity. Within the framework of Boltzmann transport equations and relaxation time approximation, the electrical conductivity, Seebeck coefficient, electronic thermal conductivity, and the lattice thermal conductivity is obtained. Simulation results indicate that TE properties of the rough InN/GaN core-shell NWs are strongly affected by the surface roughness and the diameter of NWs. The optimized condition of the proposed rough InN/GaN core-shell TE NWs is studied in this paper and the highest ZT obtained in the calculation is 0.8598 at 300 K and 1.713 at 1000K.