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A practical method to measure spin axis position of superconducting sphere rotor in cryogenic instrument using a reflective intensity modulated optical fiber sensor is presented. The deviation amount and direction of the spin axis are obtained by calculating the amplitude and phase of the reflective optical intensity signal. The experiments are carried out for the verification of the theoretical model and the performance evaluation of the sensor system. The experimental results show that the resolution, repeatability and linearity of the sensor system can achieve 10 ??m, 2% and 0.9988 respectively.