The damage of aqueduct structures caused by earthquake disaster is influenced and restricted by various factors. The randomness in concrete mechanical properties and seismic excitations are two of the significant factors that may alter the failure modes of aqueduct structures. To this end, this paper carried out systematically the random dynamic response analysis of aqueducts subjected to the above two coupled randomness condition. Further, the anti-seismic reliability analysis method for aqueducts considering the coupled randomness from both structural parameters and excitations is developed taking a large aqueduct structure as an example. The basic research principles and application approaches of the developed framework were illustrated in detail based on the probability density evolution theory. The results show that the displacement response of the aqueduct structure under the coupled randomness condition intensifies obviously, and the residual deformation and displacement variability of the displacement response are larger than that caused by the single randomness earthquake condition. With the decrease of threshold value, the gap between the reliability of aqueduct structure under coupled randomness condition and that under single randomness earthquake condition is increasing, and the reliability of aqueduct structure under the above two conditions is decreasing continuously.