Research on ecological compensation standard is a challenging topic in the field of river basin management. We estimated the cross-boundary pollution caused by pig breeding in Jiuzhou River Basin as a case study, and calculated the total amount of pollutant reduction based on pollutants control targets of COD, TP, and TN. In the estimation process, we set up three typical control scenarios, which included: closing pig farms in forbidden breeding areas, transforming bed breeding mode, and central treating of wastewater. Considering the pollutant reduction target as the principal constraint, a linear programming model was conducted to calculate the input cost of water pollution control under different treatment scenarios; we also modelled the minimum ecological compensation based on these scenarios. Taking the water consumption, water supply and GDP as the main constraints, we established a compensation analysis with the certain proportion of investment from central government, local government of Guangdong and Guangxi province; therefore, the ecological compensation amount of each side was determined based on their investment. In this research, Monte Carlo simulation and sensitivity analysis was applied to estimate the uncertainty of parameters while modelling compensation. All possible values and variance contribution rates to ecological compensation under uncertain model parameters were calculated, these parameters included breeding volumetric ratio (k1), wastewater discharge to river basin in forbidden zone (k2), and daily wastewater discharge amount with loft-bed (k3) and daily wastewater discharge amount under traditional breeding case (k4). Our results show that: (1) the reduction amount of total pollutants for COD was 378752.98 t, 2161.60 t for TP reduction and 13951.70 t for TN reduction under 90% guarantee rate of water quality standard; (2) total amount of ecological compensation was 1.503 billion based on the cost accounting method, and the allocation amount of the central government, local government of Guangxi and Guangdong province was 376 million, 331 million and 796 million, respectively; (3) under the confidence intervals level of 95%, the ecological compensation values in two different scenarios were calculated as 1.25-1.74 billion and 0.93-2.19billion. (4)refering to the sensitive analysis of parameters, the variance contribution rates of parameters k1, k2 and k3 was 79.50%, 18.90% and 1.60%, separately in scenario 1, and 88.80% of parameter k2 and 11.20% for 44 in scenario 2.