Regarding the displacements and internal forces of Timoshenko beams as dual variables, Timoshenko beam problems were included into dual variables system. Corresponding to state transfer solution of Hamiltonian dual equation, transfer form solution of dual variables for Timoshenko beams was presented. Based on transfer form solution, element stiffness equation and the shape functions of Timoshenko beams were deduced, boundary integral equation and the fundamental solution function of Timoshenko beams were obtained, which reveal the intrinsic relationships among the finite element method, the boundary element method and dual variables system of Timoshenko beams. Based on the transfer form solution of Timoshenko beams, transfer matrix method for chain structure of Timoshenko beams was proposed. For chain beam structure problems, transfer matrix method is simple, intuitive, and has the advantages of good boundary adaptability and less calculation in solving the node variables of chain structures with recursive solution. The numerical results demonstrate the feasibility and accuracy of transfer matrix method in complex beam structure problems.