Abstract Water scarcity causes conflicts among natural resources, society and economy and reinforces the need for optimal allocation of irrigation water resources in a sustainable way. Uncertainties caused by natural conditions and human activities make optimal allocation more complex. An intuitionistic fuzzy multi-objective non-linear programming (IFMONLP) model for irrigation water allocation under the combination of dry and wet conditions is developed to help decision makers mitigate water scarcity. The model is capable of quantitatively solving multiple problems including crop yield increase, blue water saving, and water supply cost reduction to obtain a balanced water allocation scheme using a multi-objective non-linear programming technique. Moreover, it can deal with uncertainty as well as hesitation based on the introduction of intuitionistic fuzzy numbers. Consideration of the combination of dry and wet conditions for water availability and precipitation makes it possible to gain insights into the various irrigation water allocations, and joint probabilities based on copula functions provide decision makers an average standard for irrigation. A case study on optimally allocating both surface water and groundwater to different growth periods of rice in different subareas in Heping irrigation area, Qing’an County, northeast China shows the potential and applicability of the developed model. Results show that the crop yield increase target especially in tillering and elongation stages is a prevailing concern when more water is available, and trading schemes can mitigate water supply cost and save water with an increased grain output. Results also reveal that the water allocation schemes are sensitive to the variation of water availability and precipitation with uncertain characteristics. The IFMONLP model is applicable for most irrigation areas with limited water supplies to determine irrigation water strategies under a fuzzy environment.