In the control of open-channel, it is difficult to estimate wave propergation time because of the complexity of reflection, superposition and energy attenuation of shallow water waves. Although Saint-Venant equation have reasonable accuracy in describing the motion law of unsteady flow, mathematically it is the first order quasilinear hyperbolic partial differential equations which makes it difficult to be used as control model in the design optimized controller. The Channel Integrator Delay Zero (IDZ) model linearizes the Saint-Venant equation and ensures the accuracy of the response of water level and discharge in high frequency band. However, there is still a considerable difference between the theoretical value and the actual response. In order to avoid this difference caused by theoretical derivation, this paper uses the single channel model of Zhanghe Irrigation District to play online identification of the relevant parameters by using the existing periodic response process of the canal system. The reliability of model identification under step water intake is verified, and the effect of this method on periodic water intakes in long channel is verified. The results show that the identified model can catch most dynamic action of the canal system with water intakes, which ensures its validity to be used for controller design. Meanwhile, it is simple in application.