Abstract: In view of the nonlinearity and complexity of Muskingum flood routing model，a new method of parameter estimation for Muskingum routing model based on Immune Clonal Selection Algorithm（ICSA） is proposed in this paper.The results of simulation experiment and application show that ICSA has many good properties such as fast computing speed，high accuracy，easy control variables setting，high universality and etc.Compared with the other parameter estimation methods of Muskingum routing model，ICSA has the best performance.So ICSA can be used as an efficient method for parameter estimation of Muskingum routing model，furthermore，it can be widely applied to optimize varieties of flood forecast model.