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Water and land are the two most critical resources for food production and they are intricately linked. Irrigation expansion, population growth, and climate change are threatening the sustainability of water-land nexus system (WLNS). In this study, a possibilistic-flexible chance-constrained programming (PFCP) method that is capable of addressing multiple uncertainties expressed as possibilistic distributions, flexible variables, and probabilistic distributions existed in WLNS is developed. PFCP can help gain in-depth analysis of the tradeoffs between system benefit and reliability of satisfying constraints. Then, the proposed PFCP method is applied to the lower reaches of Amu Darya River basin for assessing the impact of irrigation efficiency on the WLNS management, where 1080 scenarios are analyzed in association with different irrigation schemes, violation risk levels, and satisfactory degrees. A number of water and land resources allocation alternatives for different irrigation districts and crops are generated. Results indicate that the advanced irrigation modes (e.g., sprinkle and drip) can improve irrigation efficiency and raise unit water benefit from 0.15 US$/m(3) to 0.24 US$/m(3). Irrigation mode with efficiency of about 0.61 is an effective option in adaption to changed water availabilities, which is beneficial for pursuing balance between water and land relationships. These findings can support decision makers implementing comprehensive agricultural management strategies (e.g., the advancement of irrigation modes as well as the optimization of water and land allocation patterns) in responding to variations in water availability, electricity consumption, and market price.