Due to the immature of the p-type GaN IMPATT manufacturing process, an In04Ga06N/GaN n-ntype heterostructure was proposed to replace the conventional p-n structure, and made the GaN IMPATT diode work in IMPATT mode. The noise characteristics of the n-n type In04Ga06N/GaN IMPATT diode were studied and compared with the conventional GaN based p-n junction IMPATT diode under the same conditions. The results showed that the noise characteristics of the device with different bias current density and different thickness of InGaN layer were better than those of conventional p-n structure. Combined with the RF output characteristics of the device, it could be found that the In04Ga06N/GaN homo-heterojunction IMPATT device was not only superior to the GaN p-n structure in power and efficiency, but also superior to the conventional GaN p-n structure in noise performance, especially in the high frequency band. This work could provide more ideas and references for the design of GaN based IMPATT devices.