GaN Schottky diodes show great potential in high-power terahertz frequency multipliers. The thermal characteristics of GaN Schottky diodes with single and double-row anode arrangements are described in this paper. The temperature distribution inside the Schottky diode is discussed in detail under the coupling condition of Joule heat and solid heat transfer. The effects of different substrates and substrate geometric parameters on the thermal characteristics of the Schottky diode chips with single and double-row anode arrangements are systematically analyzed. Compared with that of the chip with single-row anode arrangement, the maximum temperature of the chip with double-row anode arrangement can be reduced by 40 K at the same conditions. For chips with different substrates, chips with diamond substrates can withstand greater power dissipation when reaching the same temperature. The simulation results are instructive for the design and optimization of Schottky diodes in the terahertz field.