The thermal stability of F ion-implanted isolated AlGaN/GaN heterostructures was investigated, with B ion-implanted isolation shown for comparison. The sheet resistance of as-implanted samples with F ions was lower than that with B ions due to enhanced hopping conduction. The leakage current for both implanted samples initially decreased and then increased with increases in post-annealing temperature, indicating a damage-induced isolation mechanism. Leakage reached a minimum value after 400°C annealing, which was over 108 times lower than the saturated current (Isat) of the as-grown structure, suggesting a successful isolation. After relatively high-temperature annealing, the leakage for F implantation showed a small change, whereas that for B implantation showed significant increase, suggesting that F-implanted isolation exhibited excellent thermal stability. Leakage current measured at 300°C for F ion-implantation was 103 times lower than the Isat of the as-grown structure, demonstrating that F ion isolation was applicable up to 300°C. Differences in current and activation energy (Ea) between the high-resistance GaN layer and F or B ion-implanted samples indicated that the leakage current originated from the region above the high-resistance GaN layer. Variation in Ea revealed that the optimal contributing states for conduction changed with operating temperature, annealing temperature, and ion species.