A double-positions 4-PPPS parallel mechanism is used for the aircraft fuselage assembly process to improve the docking efficiency and reduce the labor intensity. However, the accuracy is hard to guarantee, for the mechanism is large and redundant and has manufacturing and assembly errors. To improve the accuracy of the 4-PPPS parallel aircraft fuselage docking system, firstly, an averaging iteration method is proposed to calibrate the datum points in the airplane coordinate which are the references of the entire docking system. And secondly, a kinematic calibration method based on the derivative of the spatial pose transformation is proposed to calibrate up to 42 kinematic parameters. By these two methods, the final maximum position error reduced from 2.2 mm to 0.035 mm and the maximum pointing error reduced from 0.08 degree to 0.018 degree. The accuracy measurement and docking experiment prove the efficiency of the proposed methods.