An optical fiber magnetic field sensor has the technical advantages of strong anti-interference ability, miniaturization, and low cost. An optical fiber three-dimensional magnetic field sensor based on a magneto-optical crystal is proposed, in order to achieve the measurement of the space magnetic field vector. Moreover, a three-dimensional fiber optic vector of a magnetic field sensor probe has been designed, constructed, and experimentally demonstrated. The non-orthogonal error of the three-dimensional fiber optic vector of a magnetic field sensor is analyzed, and through the accurate measurement of the angle between the three sensing units of the optical fiber three-dimensional magnetic field sensor based on magneto-optical crystal, the system's three-axis non-orthogonal error is calibrated and compensated. The experimental test device uses a pair of energized coils to build a one-dimensional magnetic field, and calibrate the three-dimensional optical fiber with the three-dimensional magnetic field sensor system. The three-axis calibration accuracy is 0.19°, 0.26°, and 0.22°, respectively. The experimental results show that the three-dimensional magnetic field sensor based on magneto-optical crystal fiber can measure the magnetic field vector based on the resolution of 0.2 μT magnetic field intensity and 0.5° angle resolution.