Inhomogeneous materials, variable foundations, non-uniform cross-sections, and non-uniformly distributed loads are common in engineering structures and typically complicate their mechanical analysis considerably. This paper presents an accurate and efficient numerical method for the dynamic analysis of non-uniform functionally graded beams resting on inhomogeneous viscoelastic foundations subjected to non-uniformly distributed moving load and investigates the effects of non-uniformities and inhomogeneities on material, foundation, and load. Based on the Timoshenko beam theory and a Chebyshev spectral method, a consistent discrete dynamic model is derived, which can deal with all axially varying properties. A series of numerical experiments are carried out to validate the convergence and accuracy of the proposed method. The results are compared with those obtained through finite element analysis or in the literature, and excellent agreement is observed. Then, the dynamic response of an axially functionally graded beam resting on an inhomogeneous viscoelastic foundation and subjected to a non-uniformly distributed moving load is investigated. The results show that the material gradient and the inhomogeneous foundation can alter the vibration amplitudes and critical speeds of the beam significantly. Compared with more realistic non-uniformly distributed moving load models, idealized concentrated and uniformly distributed moving load models produce apparent computation errors in vibration amplitudes.