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We theoretically investigate the resonance of third harmonic generation (THG) that has been observed at frequency being half of the superconducting gap in a multiband disordered superconductor NbN. The central question is whether the dominant contribution to the THG resonance comes from the Higgs mode (the collective amplitude mode of the superconducting order parameter) or quasiparticle excitations. To resolve this issue, we analyze a realistic three-band model with effective intraband and interband phonon-mediated interactions estimated from first-principles together with nonmagnetic impurity scatterings. Using the estimated pairing interactions with multiband impurity scattering rates being varied from clean to dirty regimes, we calculate the THG susceptibility for NbN in a channel-resolved manner by means of the BCS and self-consistent Born approximations. In the dirty regime, which is close to the experimental situation, the leading contribution is given by the paramagnetic channel of the Higgs mode having almost no polarization-angle dependence, while the second leading contribution comes from the paramagnetic channel of quasiparticles generally showing significant polarization-angle dependence. The result is consistent with the recent experimental observation of no polarization-angle dependence of THG, giving firm evidence that the Higgs mode dominantly contributes to the THG resonance in NbN superconductors.