Identification results of water quality model parameter directly affect the accuracy of water quality numerical simulation. To overcome the difficulty of parameter identification caused by the measurement’s uncertainty, a new method which is the coupling of Finite Difference Method and Markov Chain Monte Carlo is developed to identify the parameters of water quality model in this paper. Taking a certain long distance open channel as an example, the effects to the results of parameters identification with different noise are discussed under steady and un-steady non-uniform flow scenarios. And also this proposed method is compared with finite difference method and Nelder Mead Simplex. The results show that it can give better results by the new method. It has good noise resistance and provides a new way to identify water quality model parameters.