Six-axis force sensors based on Stewart platform necessitate highly accurate, sensitivity and dynamic response. In response to this need, errors analysis and compensation of the force sensor are essential. In this paper, the measurement error generated by the upper platform deformation is discussed and evaluated. Furthermore, in order to improve the precision, a real-time compensation algorithm is proposed depending on the external force applied on the force sensor. Finally, a numerical simulation example is presented, which indicates that the precision is related to the stiffness of limbs directly and improved obviously by the compensation algorithm.