A fine system-level calibration technique of size effect error is presented for Fiber-strap-down inertial navigation systems (Fiber-SINS) in this paper. When the strap-down system is mounted onto high precision turntable and rotating along predefined trajectory, the velocity errors can contain information related to the size effect error, which can be estimated accurately by Kalman filter. In this paper, principles of the calibration technique are emphasized, the model of the size effect error is presented and Hardware-in-the-Loop Simulation platform is designed to validate the efficiency of this technique. Results show that the calibration technique has the advantages such as simplicity and high precision. Thus it is of great importance for practical applications.