Normal tissues may be damaged due to the high temperature if heated by continuous microwave. We proposed that the temperature distribution of heated area inside the bio-tissues could be effectively controlled if the bio-tissues is radiated by pulse modulated microwave coded with computer. Infrared thermography was applied to image temperature distribution of sliced homogeneous simulating biomaterial. Effects of temperature distribution in heated area of bio-tissues were analyzed and discussed while duty cycle, power and frequency of pulse modulated microwave were changed. The results showed that raising the duty ratio and power, or changing frequency in certain range can make distinct heating effects in bio-tissues. It provides a new effective heating method for tumor hyperthermia.