Water rights transaction has proved to be an effective method for constructing an efficient water distribution system (WDS) in various regions of the Yellow River Basin (YRB). In this study, an optimal WDS in the YRB is proposed by considering the comprehensive value of water resources, administrative management system, and market-based system. To accurately quantify the comprehensive value of water resources, the work analysis method of suspended load and bedload based on the emergy theory and time-averaged motion equation is introduced, and the quantification process of sediment transport value in the river course is formulated in the YRB. Based on this, an administrative and market-based game for water rights transaction is formulated. In this double-layer game model, the administrative authorities of the basin (Yellow River Conservancy Commission) and the corresponding regions (Water Resources Department) seek to maximize their own target revenue function/comprehensive value of the water resources. Then, the optimal trading quantity of water in each region and the bargain price can be solved. A case study is presented in the YRB to verify the effectiveness of this method. The results reveal that (1) the error rate of the riverbed shear stress as well as the sediment transport rate between the theoretical value and the calculated value does not exceed 8.76%, which indicates the rationality of the calculation method of sediment transport value; (2) the proposed dynamic differential game and pricing game perform well in determining the optimal trading quantity of water in each region. They also reveal the bargain price with optimal results of ¥ 4151.1456 half yearly and ¥ 8197.3466 per year in 2018, outperforming other methodologies.