In order to improve the calculation efficiency of the seismic dynamic time-history analysis for rigid frame bridge with variable cross-sections, a calculation method was established based on the discrete time transfer matrix method. Firstly, employing the linearization method of step-by-step time integration method, the element transfer matrix was derived based on the dynamic equilibrium equation of Euler beam, whose transverse displacement was described by modal coordinates. Secondly, according to the principle of tensor computation, the construction method of the whole transfer matrix for the discrete system of rigid frame bridge with variable cross-sections was derived by means of the coordination matrix and the equilibrium matrix at the bifurcation point. Finally, utilizing the numerical simulation software, the seismic dynamic time-history analysis of rigid frame bridge with variable cross-sections under multiple-support seismic inputs was realized using numerical iteration. Taking a rigid frame bridge with variable cross-sections as an example, the reliability and high computational efficiency of the proposed method were verified by the numerical results as compared to the finite element method.