Abstract: In comprehensively consideration of the factors of the population, the socio-economic development and the environmental governance level, taking pollution emissions and contribution rate of pollution per unit flow to the water quality of target section as indicators, this paper builds a water environmental capacity and pollutants allocation model based on the principle of fairness, efficiency and incentive of environmental governance. Water environment capacity allocation for Laixi River (Rongchang Section) was conducted by using the model. The results indicated that the residual water environmental capacity of CODcr and NH3-N in the watershed increased 266.9t/a and 63.2t/a than that in traditional equal-probability allocation. The target emission reductions were more fairness and easily accepted. This study can provide theoretical basis and technical assistance for the total pollutants’ control work, which is important for the fine management of the watershed.