The temperature variation characteristic of the input axis misalignment angle of fiber optic gyro has become one of the key problems of orthogonal calibration of the fiber optic gyro inertia system. Firstly, a kind of measurement method, which can eliminate the measurement errors effectively, was presented. Then, the input axis misalignment angles of three fiber optic gyros with elliptical-structure optical fiber rings were measured. It is found that the three samples have similar input axis misalignment angles; the input axis misalignment angles vary non-monotonously with the changing of temperature; and the varying velocity is fast relatively in high temperature region. The results may be useful for improving the manufacturing technology of the fiber ring of the fiber optic gyro and will be helpful to prompt the temperature compensation technology of the orthogonal calibration in fiber optic gyro inertia system.