This paper develops a versatile and effective force-density framework for the flexible multi-body dynamic analysis of clustered tensegrity structures. In this framework, the force density is selected as the basic variable instead of force, and the clustered tensegrity structure is mathematically described in a vector and matrix form, encompassing topology, geometry, material, and force properties. A non-negative variable is defined as an indicator of the member stress state, and a complementary function is constructed to address the discontinuity issues that arise from the unidirectional axial stiffness of cables. Dynamic formulas are established within this force-density framework, with nodal coordinates selected as generalized parameters and formulations constructed in a matrix form. A complementary framework is established as an alternative for solving the dynamic equations, transforming the isolated steps of Newton’s iteration and cable state judgment (slack or tension) into a unified one, bringing more potential for improving solving efficiency. Numerical simulations are carried out to validate the approach, demonstrating that it effectively reveals the dynamic oscillation, tension changes, and cable slack behavior of clustered tensegrity structures during shape control. Comparative studies highlight the advantage of computational efficiency. The method proposed in this paper provides a robust mathematical model for studying clustered tensegrity structures, particularly regarding the shape control of deployable, active, and intelligent structures, aiding in understanding dynamic oscillation, tension changes, and cable slack behavior during their deformation. The methods can also be applied to cable net structures and other prestressed pin-jointed systems.