The invention discloses a midpoint generalized watercourse pollution-holding capability risk estimation and planning rationalization promotion method. The method includes the following steps that firstly, whether a pollution-holding river segment planned sewage outlet is suitable for sewage outlet midpoint generalization or not is determined, and the pollution-holding capacity of the river segmentis calculated; secondly, the initial section position x, the standard control section position x' and the initial section pollutant concentration C0 of the river section are determined, and the average flow speed u of the river section and the watercourse flow Q are measured; thirdly, according to the measurement result, the pollutant degradation coefficient k and the uncertainty alpha of the river section are determined; fourthly, the standard pollutant concentration Cs of a control section is determined, and the variance D(W) of the pollution-holding capability of the river section is calculated; fifthly, according to the variance D(W) of the pollution-holding capability and the planned pollution-holding capability, uncertain risks of the watercourse pollution-holding capability are determined, and planning rationalization is promoted by using the result. By means of the method, uncertain risks caused by uncertain degradation coefficient in a watercourse to pollution-holding capability calculation can be effectively estimated, watercourse water quality planning rationalization is promoted, and the method is easy to popularize in various kinds of watercourse water quality management.