The use of equivalent beam models to estimate the dynamical characteristics of complex tall buildings has been investigated by several authors. The main reason is the structural response estimation to stochastic loads, such as wind and earthquake, using a reduced number of degrees of freedom, which reduces the computational costs and therefore gives the designer an effective tool to explore a number of possible structural solutions. In this paper, a novel approach to calibrate the mechanical and dynamical features of a complete 3D Timoshenko beam, i.e., describing bending, shear and torsional behavior, is proposed. This approach is based on explicitly considering the sub-structures of the tall building. In particular, the frames, shear walls and lattice sub-systems are modeled as equivalent beams, constrained by means of rigid diaphragms at different floors. The overall dynamic features of the tall building are obtained by equating the deformation energy of an equivalent sandwich beam with that of the selected sub-structures. Finally, the 3D Timoshenko equivalent beam parameters are calibrated by minimizing a suitable function of modal natural frequencies and static displacements. The closed form modal solution of the equivalent beam model is used to obtain the response to stochastic loads.