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At present, the shortage of water resources has become a serious constraint to the further development of social economy. The optimal allocation of multi-water resources is valuable for agricultural water management in arid and semi-arid regions. However, traditional deterministic programming does not solve the complex water resources allocation in irrigation systems. Furthermore, previous allocation methods of irrigation water seldom considered the water cycle process, especially for multi-sources of irrigation. In this study, we develop an inexact fuzzy stochastic simulation-optimization programming (IFSSOP) model for the irrigation water optimal allocation of two water sources. The model combines the crop water model and the field water cycle model with an uncertainty optimization model, which considers the contribution of groundwater to crop water consumption. As a case study, the developed model is used in an arid area with two irrigation water sources: a river and a lake. Accordingly, the total optimal allocation irrigation water amounts of river and lake water under different violation probabilities in various hydrological years were obtained. By comparing the IFSSOP model with the IFSSOP model without considering the contribution of shallow groundwater (IFSSOP-NG model), it can be shown that the system benefits of the developed model are higher. With the lake water source from flood water, the region can save 30-34% of the river water, maintaining the original crop water deficit irrigation ratio. Consequently, application of the IFSSOP model in irrigation scheduling will provide effective water allocation patterns to save more water in an arid region with shallow groundwater.