Wurtzite GaN epilayers irradiated at room temperature with 308 MeV 129Xe35+ ions to fluences of 1 × 1013 and 3 × 1013 cm−2 have been studied by contact mode atomic force microscopy (AFM), high-resolution X-ray diffraction (HRXRD), micro-Raman scattering and photoluminescence (PL) spectroscopy. The AFM images showed that the surface of GaN films was etched efficiently due to the Xe ion irradiation. The initial step-terrace structure on GaN surface was eliminated completely at a fluence of 3 × 1013 cm−2. HRXRD and Raman results indicated that the Xe ion irradiation led to a homogenous lattice expansion throughout the entire ∼3 μm-thick GaN films. The lattice expansion as well as the biaxial compressive stress of the films was increasing with the increase of ion fluence. PL measurements showed that a dominant yellow luminescence band in the as-grown GaN films disappeared, but a blue and a green luminescence bands were produced after irradiation. Based on these results, the strong electronic excitation effect of 308 MeV Xe ions in GaN is discussed.