Internal temperature equalization of cortical bone and cancellous bone by microwave irradiation were investigated. Equality of heating velocity and internal temperature in femoral head of bovine and diaphysis of bovine femur was measured, and experimental model to control temperature and time by microwave irradiation was determined. Insert head of optical fiber thermometer into the hole of bovine's bone (femur diaphysis and femoral head). And measured temperature after heated in microwave oven. As bone was heated from inside by using microwave irradiation, the bone was heated more rapidly and faster than regular thermal process method. Moreover, humidifying the surface of bone resulted temperature of entire bone to keep close temperature of inside of bovine's bone (femur diaphysis and femoral head). Results show that the thermal processing method using microwave irradiation seems to be effective for disinfections if equality of temperature is improved further.