The measuring probe integrated with multiple fiber point-diffraction sources can be applied to measure both the three-dimensional coordinates and highly accurate point-diffraction wavefront. The probe determines the achievable measurement accuracy of fiber point-diffraction interferometer (PDI), in which the fiber exit end plane is required to be parallel with the detector plane. The probe misalignment due to fabrication error could introduce significant measurement error. A high-precision method is proposed to calibrate the probe misalignment in fiber PDI, including the central positioning based on phase difference and tilt adjustment based on Zernike polynomials fitting. Both numerical simulation and experiments have been carried out to demonstrate the feasibility and accuracy of the proposed probe misalignment calibration method. The proposed method provides a feasible way to address the processing uncertainty on measuring probe in fiber PDI, and enables high-precision geometry alignment and misalignment calibration in the interferometric testing systems with case of no imaging lens.