Continuous wave (CW) laser-induced temperature rise is studied in Raman spectra of nanocrystalline-silicon (nC-Si) films on quartz and sapphire substrates. The zone-center-phonon (ZCP) mode in the Raman spectra shows remarkably different frequencies in the thin films as the incident CW laser power density is increased (always kept lower than that used during annealing). For the films on the quartz substrate, the prominent ZCP mode shows a rather large phonon softening from 517 to 485 cm−1. The phonon softening in the nC-Si film on sapphire substrate was from 517 to 508 cm−1. In order to see the role of laser heating, we have also computed the temperature rise in the two films by employing Green's function heat diffusion equations for the two-layered structures. We could ascribe the differences in laser-induced phonon softening in the two films to the rise in temperatures. Good agreement between temperatures obtained by Raman data and heat diffusion equation is achieved here.