The radiofrequency ablation temperature system is characterised by its time-varying, non-linear, and hysteretic nature. The application of PID controllers to the control of radiofrequency ablation temperature systems has a number of challenges, including overshoot, dependence on high-precision mathematical models, and difficulty in parameter tuning. Therefore, in order to improve the effectiveness of radiofrequency ablation temperature control, an adaptive network-based fuzzy inference system combined with an incremental PID controller was used to optimise the shortcomings of the PID controller in radiofrequency ablation temperature control. At the same time, the learning rate at the time of updating the consequence parameters was set by segmentation to solve the problem of poor control accuracy when the ANFIS-PID controller is implemented based on FPGA fixed-point decimals. Based on FPGA-in-the-loop simulation experiments and ex vivo experiments, the effectiveness of the ANFIS-PID controller in the temperature control of radiofrequency ablation was verified and compared with the PID controller under the same conditions. The experimental results show that the ANFIS-PID controller has a superior performance in terms of tracking capability and stability compared with the PID controller.