In order to obtain the dynamic characteristics of the overall structure of aqueduct, the modal tests of ambient excitation were conducted by the oneway SIMO method and the twoway MIMO method. Longitudinal, transverse, vertical and transversevertical bidirectional modal parameters were identified by the enhanced frequency domain decomposition. The results show that most spectrum peaks have been obviously identified by two methods with satisfactory dentification results of modal parameters. The longitudinal modes and first four transverse modes of aqueduct structure are dominated by the vibration of the bent structure, and the aqueduct body is the translation or rotation or motionless. After the fifth transverse modes, most of them are dominated by the aqueduct body, and the bent structure is barely moving or vibrates very little. The vertical modes are dominated by the vibration of aqueduct body. In addition, the bidirectional modes identified by the MIMO method include both the transverse and vertical components, and the errors of modal frequency identified by both the SIMO and MIMO methods are small. According to the identification accuracy and comprehensive information of modal tests, the twoway MIMO method is better than the oneway SIMO method for the overall structure of aqueduct.