The earthquake responses are studied for the tall flexible structures such as TV towers when the vertical eccentricities between the discrete nodes and the corresponding centroids of investigated lumps are considered. In practical analyses, the tall flexible structures can be made into a spatial-discrete system of some certain length of beam elements with different lengths and cross-sectional areas. These elements are used to construct the investigated lumps in this paper. The different cross-sectional areas and the different lengths of two adjacent elements lead to the appearance of vertical eccentricity between the discrete node and the centroid of investigated lump within the same investigated lump. Firstly, the governing equations are established for a typical investigated lump. Secondly, the calculating formulae of the forces and moments acting on the investigated lump are derived and provided. Finally the new dynamic equilibrium equations with modified mass matrix and assemblage of stiffness matrix have been derived for the stick MDOF model based on beam theory when the existing vertical eccentricities are considered. Numerical results demonstrate that these vertical eccentricities should be considered in order to obtain the accurate earthquake responses for the tall flexible structures.