We obtained a 40-pair Si-doped n-type conducting AlInN/GaN distributed Bragg reflector (DBR) with a low surface pit density, 3.0 × 106 cm−2, by introducing 5 nm Si-doped Al0.39Ga0.61N graded layers grown at high temperature, 1150 °C. A combination of a 0.6 nm GaN cap layer on AlInN and a subsequent thermal cleaning during a temperature increase process up to 1150 °C for the following AlGaN graded layer growth was effective for a suppression of pit/threading dislocation generations at the interfaces of the AlInN layers and the AlGaN graded layers in the DBRs without any additional cleaning processes. We also found that an initial AlN mole fraction of 0.39 in the graded AlGaN layers provided the lowest vertical resistance of the Si-doped AlInN/GaN DBRs with the Si-doped AlGaN graded layers, suggesting that Al0.39Ga0.61N provides the lowest potential spike in the conduction band of the interface with Al0.82In0.18N among AlGaN alloys.