Aiming at the issue of significant uncertainty in the process of emission trading due to changes in factors such as water pollution carrying capacity, pollution load, and protection goals, interval programming theory was introduced to seek the optimal solution considering these uncertain factors. The MIKE11 model was used to simulate the water quantity and quality process of the Shaying River, and the pollutant carrying capacity process of each water functional area under different inflow conditions was obtained. The environmental capacity model was used for initial allocation of emission permits, the emission permit trading model based on interval planning and multi-objective optimization solution method were proposed, and the interval values of emission permit trading for each calculation unit under different operating conditions were obtained. The results show that in the optimized emission trading plan, the economic benefits of the Shaying River Basin increase by 5820.66 million to 12176.02 million yuan, the remaining environmental capacity is 0 to 16948t/a, and the water quality compliance rate increases by 85% to 90%. The scheme selected through interval planning can reflect the uncertainty factors of emission trading and reduce the impact of changes in various constraints during the trading process.