Fiber optic gyros (FOGs) are sensitive to the environment fields where they are mounted, and their drifts are easily affected when surrounding temperature field or magnetic field changes. In FOG strapdown inertial navigation system (INS), gyro drifts caused by environmental fields are stable mostly, thus they could be calibrated and compensated beforehand and would not cause obvious alignment and navigation errors. However, in rotation INS (RINS), although navigation errors caused by the constant components of FOG drifts could be well attenuated, the gyro sensing axes are changing relative to the environmental fields in the RINS, which would lead to periodically changing gyro drift components when inertial measurement unit is pointing to different headings, thus producing serious alignment and navigation errors in FOG RINS. To solve this problem, a four-position heading effect calibration algorithm was proposed, and its effectiveness and validity were verified through a dual-axis FOG RINS by turntable experiments. The experimental results show that the azimuth alignment accuracy of the FOG RINS improves from 0.2 deg to about 0.04 deg, increasing five times approximately, which illustrates that the proposed heading effect calibration algorithm could further improve the navigation performance of FOG RINS significantly.