The thermal transport process of measuring probes within PET cyclotron is simulated based on finite difference time domain (FDTD) method. For both dynamic and static measurement modes, the highest surface temperature and back-end temperature for three probes of different (Cu, Ta, W) are obtained with the variation of power load time under thermal irradiation condition. The results show that there is no obvious difference among the three materials and the speed of probes should be 10 mm/s in dynamic mode. However, in static mode, copper turns out to be the best material for probe design due to its advantages such as high blackness and high thermal conductivity.