This work investigates the phonon properties such as phonon dispersion relation, average group velocity, and phonon density of state (DOS) theoretically in GaN nanofilm under various surface stress fields. By taking into account of the surface energy effects, the elasticity theory is presented to describe the confined phonons of nanofilms with different surface stresses. The calculation results show that the influence of surface stress on the phonon properties depends on the thickness of nanofilm. The negative surface stress leads to a higher average group velocity and corresponding lower phonon DOS. The positive surface stress has the opposite effect. The significant modification of thermal properties, e.g., phonon thermal conductivity, in GaN nanofilms is mostly stemmed from the change of phonon average group velocity and DOS by surface stress. These results suggest that the thermal or electrical properties in GaN nanofilms could be enhanced or reduced by tuning the surface stress acting on the films.