Ion beam bombardment of proton, He+, Ar+, Xe+ ions were made on single crystal substrate by cyclotron. The GaN epi-layer material was grown by MOCVD on ion beam bombarded substrate. After deposition of GaN epi-layer heat treatment was made in flow of N2. The RMS roughness of the substrate was increased by ion bombardment. The GaN crystal quality for substrates of ion bombardment was better than that for bare substrates. Raman spectrum analysis indicated the induced stress in the GaN epi-layer during the heat treatment. The electrical property of GaN was improved after heat treatment. It is estimated that ion bombardment of proton with current of 1μA is the optimum condition in our experimental condition.