In this paper, dynamic characteristics analysis is carried out for a large aqueduct of South-to-North Water Transfer Project using large finite element analysis software. Two kinds of connection supports are considered, namely elastic support and completely simple support. Six kinds of water depths are calculated by additional mass method: empty aqueduct, 1/4 water depth, 1/2 water depth, 3/4 water depth, designed water depth, full water depth. Results show that basin type rubber support strengthens the constraint to aqueduct, and strengthens the connection of aqueduct to pier, and also increases the system stiffness, therefore the natural frequency is higher than that of completely simple support; The influence of water to dynamic characteristics of the aqueduct is quite obvious, so water effect must be considered in computation; Water has no influence on the principal mode shapes of the aqueduct structure, i.e. the dry mode shape and the wet mode shape are similar in appearance.