Capacitance-voltage (C-V) measurement is an effective method that has been widely used to study the electronic characteristics of the pn junction. In this paper, the C-V measurement is used to study the effect of the temperature on the structural type of the GaN-based pn junction. The C−2-V and C−3-V curves, combined with power-law index k, are used to determine the structural type of the GaN-based pn junction when the temperature is set at 25 °C, −50 °C, −100 °C, −150 °C, and −195 °C. Our experimental results show that the C−2-V curve is a clear linear relation, and the index k is 0.5 when the temperature is set at 25 °C and −50 °C. This shows an abrupt junction when the temperature ranges from 25 °C to −50 °C. When the temperature is dropped to −100 °C, the structural type of the pn junction begins to change and the index k becomes 0.45. When the temperature is decreased further to T = −150 °C and −195 °C, the index k becomes 0.30 and 0.28, respectively, corresponding to a non-abrupt and non-linear junction. Possible explanations of this phenomenon are: the low-temperature carrier freeze-out effect and the localized space charge region that is produced by crystal defects and interface states. The enhancement of the inhomogeneous and localized space charge region further affects the structural type of the pn junction in a low temperature environment.