The bolt-ball joint, which have wide application in spatial lattice structure, have too many components, so the initial defect may be caused by the screw length insufficiency of the high-strength bolt during installation process. To study the effect of the defect on the mechanical properties of these joints, a sophisticated FEM simulation model of the bolt-ball joint with thread was calculated by ANSYS. The number of thread engagement was changed to simulate the screw length of high-strength bolt, and the simulation method was verified by existing experimental data. The flexural behavior of three common joints (M20, M24, M27) under different screw length was analyzed. The result shows that the bolt-ball joints mainly have three work and failure modes when the screw length is changed. The screw length insufficiency of the high-strength bolt significantly reduces stiffness and bearing capacity of the joint. The tensile property of three joints under different screw length was analyzed, and the deterioration law of the tensile bearing capacity and the possible failure modes were found. The curve which shows the relationship between the reduced proportion of the tensile bearing capacity and the screw length was given. This study can provide technical references for the construction control of the bolt-ball joint and the safety performance evaluation of the similar structure.