Purpose The charring tissue formation in the ablated lesion during the microwave ablation (MWA) of tumors would induce various unwanted inflammatory responses. This paper aimed to deliver appropriate thermal dose for effective ablations while preventing tissue carbonization by optimizing the treatment protocol during MWA with the set combinations of temperature control and pulsed microwave energy delivery. Material and methods The thermal phase transition of ex vivo porcine liver tissues were recorded by differential scanning calorimetry (DSC) to determine the temperature threshold during microwave output control. MWA was performed by an in-house built system with the ease of microwave output parameter adjustment and real-time temperature monitoring. The effects of continuous and pulsed microwave deliveries as well as various intermittent time-set of MWA were evaluated by measuring the dimensions of the coagulation zone and the carbonization zone. Results The DSC scans demonstrated that the ex vivo porcine liver tissues have been in a state of endothermic heat during the heating process, where the maximum absorbed heat occurred at the temperature of 105 °C ± 5 °C. The temperature control during MWA resulted in effective coagulative necrosis while preventing tissue carbonization, after setting 100 °C as the upper threshold temperature and 60 °C as the lower threshold. Both the numerical simulation and ex vivo experiments have shown that, upon the optimization of the time-set parameters in the periodic intermittent pulsed microwave output, the tissue carbonization was significantly diminished. Conclusion This study developed a straight-forward anti-carbonization strategy in MWA by modulating the pulsing mode and intermittent time. The programmed protocols of intermittent pulsing MWA have demonstrated its potentials toward future expansion of MWA technology in clinical application.