In order to explore the method of promoting the agriculture sustainability in irrigation area under uncertainties through the optimization of irrigation water resources allocation, the methods of stochastic programming and multiobjective programming were used to carry out studies in Jinxi Irrigation Area in Heilongjiang Province and the following results were obtained: based on the optimization, the total irrigation water consumption was saved by 1.3×108m3 to 3.9×108m3 and the irrigation water productivity was increased by 0.85kg/m3 to 1.01kg/m3. At the same time, the agricultural economic benefitswas increased by 18×107 yuan to 69×108 yuan. The ecological water allocation was more than 4×107m3 and the reduction value of agricultural pollutant was 1.28×104 ton to 3.13×104 ton, therefore, the degree of agricultural sustainability in irrigation areas was improved effectively. Otherwise, the benefits of economic, ecological and social among the optimized irrigation water resources allocation policies had obvious differences which was caused by the influence of uncertain factors on the agriculture sustainability. The comprehensive agriculture sustainability of the optimal water allocation policies was analyzed from the aspects of economics benefits, water resources allocation equity, agricultural water resources productivity, agricultural pollutant intensity, GWP and agricultural water resources utilization ratio. Based on the above analysis, the optimal water allocation scheme under each scenario can be determined. Moreover, the sustainability degrees of optimal scheme were all more than 0.4, which meant that the optimized water resource allocation scheme can effectively enhance agriculture sustainability by stabilizing grain yield, improving the efficiency of irrigation and protecting ecological environment in the irrigation areas.