In order to improve the reliability of ammunition feeding and the stability of ammunition storage mechanism of naval gun, the dynamics analysis of ball screw transmission system of surface ship was carried out. By using the finite element analysis and rigid-flexible coupling dynamic simulation analysis method, combined with the comprehensive sea conditions of grade 6 and grade 9, the stress and strain of the ball screw pair are analyzed. The results show that the stress and strain both reach the peak value when starting, which can provide a reference for the design and strengthening of the surface ship ball screw pair.