A comprehensive calibration algorithm is proposed in this paper with the aim of solving the problem whereby the navigation error of a long-endurance shipborne grid strapdown inertial navigation system (SINS) drifts with time. First, the equation within the inertial frame is deduced to establish the relationship between the position error, the grid yaw error and the platform drift angle in the inertial frame; then in combination with the equation within the inertial frame, the calibration schemes are designed. The gyroscope drift in the body frame is estimated and compensated through the designed calibration schemes with the aid of information either on two intermittent external positions and yaw, or on three intermittent external positions. The simulation results illustrate that, in the former case, the three-axis gyroscope drifts can be estimated accurately; in the latter case, the z-axis gyroscope drift and the grid yaw error can be estimated accurately. Resetting the system error based on external navigation information and compensating the gyroscope drift can effectively restrain the accumulated navigation error of shipborne grid SINS; meanwhile the proposed algorithm is unaffected by the motion of the ship, which has significant practical value in engineering.