The surface damage of the seed crystal will lead to increased dislocations of the grown crystal. In order to reduce the damage to the surface of the seed crystal, a wafer processed by a multi-step process of rough grinding-finishing-polishing is generally used as the seed crystal. The complicated process involves many steps, and the cost is high. In this paper, the rough ground GaN with phosphoric acid to remove the surface damage layer and the chemical mechanical polished GaN were used as seed crystals respectively. The crystal surface, the growth rate, crystal quality and stress of the two seed crystals after ammonothermal growth were compared. The optical microscopy shows that the surface after the growth of the two seed crystals have similar hillocks. The growth rate of ammonothermal method is slow, and the growth rate of chemically mechanically polished seed crystal is slightly higher than that of rough ground seed crystal. The full width at half maximum (FWHM) of X-ray diffraction rocking curves of (002) and (102) planes show that the quality of GaN crystal obtained by the growth of polished seed crystal is basically the same as that of coarsely ground seed crystal. E2 (high) frequency shift of Raman indicates that the GaN crystal grown on the polished seed crystal is close to the stress-free state, and the crystal grown on the coarsely ground seed crystal has a small compressive stress.