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A finite domain time difference (FDTD) and second-derivative combined method is proposed for the evaluation of phase center in the Fresnel region of complex structure millimeter antennas. This method adopts FDTD's near to far field transformation to obtain the fields in Fresnel region and then applies the second-derivative method to calculate the phase center. The adoption of FDTD efficiently overcomes the difficulties arising from the existing calculation methods' requirements for the radiation analytical formula of some complex antennas, which makes the existing second-derivative method more applicable in engineering. Also, FDTD increases the precision owing to the superposition field calculation from its extrapolation. The correctness of this proposed method is certified with typical examples and the phase center in the Fresnel region of a microwave radiometry calibration corrugate horn antenna is evaluated with the key features.