In reality, severe water shortage crisis has made bad impact on the sustainable development of a region. In addition, uncertainties are inevitable in the irrigation system. Therefore, a fully fuzzy fractional programming model for optimization allocation of irrigation water resources, which aimed at not only irrigation water optimization but also improving water use efficiency. And then the developed model applied to a case study in Minqin County, Gansu Province, China, which selected maximum economic benefit of per unit water resources as planning objective. Moreover, surface and underground water are main water sources for irrigation. Thus, conjunctive use of surface and underground water was taken under consideration in this study. By solving the developed model, a series of optimal crop area and planting schemes, which were under different α-cut levels, were offered to the decision makers. The obtained results could be helpful for decision makers to make decision on the optimal use of irrigation water resources under multiple uncertainties.