A GaN-based p-i-n diode with vertical structure was fabricated with epitaxial method by using high quality free-standing GaN substrate. Based on studing the material structure, impurity concentration and current-voltage characteristics, the key factors affecting the performance of the vertical structure device were analyzed. Experimental results indicate that the roughness of the surface will cause the irregular shape of the annular structure, which plats a negative effect on the ohmic contact and performance of the vertical structure device. In addition, during the growth process, a variety of impurities will gather at the interface and form a planar leakage channel, which will dominantly limit the performance of the device.