The present paper proposes a new dynamic analysis method for multi-span Timoshenko beam structures supported by joints with damping subject to moving loads. An exact dynamic element matrix method is adopted to model Timoshenko beam structures. A generalized modal analysis method is applied to derive response formulae for beam structures subject to moving loads. The proposed method offers an exact and closed form solution. Two numerical examples are provided for validating and illustrating the proposed method. In the first numerical example, a single span beam with multiple moving loads is considered. A dynamic analysis on a multi-span beam under a moving load is considered as the second example, in which the flexibility and damping of supporting joints are taken into account. The numerical study proves that the proposed method is useful for the vibration analysis of multi-span beam-hype structures by moving loads.