Space manipulator has different configurations when performing space tasks,so it is difficult to realize the fundamental frequency of space manipulator under different configurations by using finite element analysis.Therefore,a calculation method based on flexibility matrix theory modeling was proposed and verified.The kinematics model was established according to the structural characteristics of the manipulator;the calculation method of the flexibility matrix theoretical modeling was proposed;the flexibility matrix theory was verified through the finite element analysis of the manipulator under two typical configurations;the ground-based fundamental frequency experiment for the manipulator was verified.The results show that the flexibility matrix calculation deviation is 3.4%,and the deviation between the theoretical analysis fundamental frequency and the finite element calculation fundamental frequency is 1%,indicating that the flexibility theoretical modeling method proposed is accurate to the fundamental frequency calculation of the mechanical arm in orbit;the deviation between the theoretical analysis fundamental frequency and the experimental fundamental frequency is 7.2%,the deviation mainly comes from the finite element simulation,which meets the engineering requirement of 10% deviation range.In this method,the flexibility matrix is combined with the manipulator configuration,the fundamental frequency of the manipulator in different configurations can be calculated quickly.Compared with the finite element method,the proposed method is greatly simplified and has some engineering application value.