A new method using ordinary differential equation (ODE) solver is applied in order to ease the dynamic analysis of tall-pier aqueduct. By simplifying the boundary conditions associated with fluid-structure interaction at pier top and considering the pier as a continuous beam instead of discretized elements, this paper converts the dynamic analysis of tall-pier aqueduct into standard forms of ODE eigenproblem and general boundary value problem, which can be solved by ODE solver based on the presented ODE eigenvalue algorithm, modal superposition and Newmark-β semi-discretization method. For illustration, two numerical examples are utilized to show the feasibility of this method to obtain dynamic characteristic, elastic seismic response and nonlinear vibration isolation response of tall-pier aqueduct. The results show that compared to the finite element method, the model and method in this paper is not only reliable, but time-saving.