There is some problems in application of WRMM model to water resource allocation in arid region in dry years.Aimed at the problem that the relationship between the penalty of WRMM model and water resources policy is not clear, through the analysis and study of penalty of WRMM model, the paper clarified the relationship between water allocation and penalty based on the principle of minimum cost under the condition of single inflow and further probed the quantity method of penalty witch is applied to a small watershed. The results is that the application effect is good, the method has important reference value for the determination of parameters in the future application of WRMM model.