In order to implement accurate water resources scheduling on the Yellow River and build a mathematical model for water regulation in accordance with the practical condition, it is necessary to provide hydrological data such as duration of flood routing on different reaches and runoff loss. Through analysis and calculation of the runoff loss in channel, this paper gives a study on the error source effecting channel runoff loss in calculation of water balance and its influence on the calculated results, and puts forward the concerned measures to control various error sources.