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• The WEF nexus is clarified based on the material flow of inputs and outputs. • A generic integrated intensity index for the WEF material nexus is proposed. • The intensity of the WEF nexus and its key aspects in the ADR basin are measured. The input–output relationships among material, energy, and information within the water, energy, and food subsystems are intricately interwoven, constituting an integrated system vital for sustainable development. Various water-energy-food (WEF) nexus indicators have been applied to evaluate the system's internal relationships and state. Nevertheless, these methods fail to aggregate the internal relationships into an indicator. This study proposes a WEF nexus indicator that incorporates the interconsumption into the system using the material flow analysis. The interconsumption consists of energy consumption in the food and water subsystems, water consumption in the energy and food subsystems, and food consumption in the energy subsystem. Moreover, the major factors were identified by the sensitivity factor method. The three countries (Tajikistan, Uzbekistan and Turkmenistan) in the Amu Darya River (ADR) basin exhibit strong interactions in the WEF nexus system, are chosen as a case study. Our results show that in 1992–2018, Uzbekistan's food subsystem consumed the most energy among the three countries; the energy consumption within the water subsystem displays an upward trend across all three countries; the water consumption in the energy subsystem of Tajikistan and Uzbekistan is 2–4 times greater than that in Turkmenistan; and the water withdrawals for agriculture within the three countries have remained relatively stable. The composite index in three countries exhibits an upward trend, with the most pronounced increase occurring in Turkmenistan. Uzbekistan has the strongest WEF nexus relationship, with a WEF nexus index that was 2–3 times greater than that of Tajikistan and Turkmenistan. The most important subsystem of Tajikistan and Turkmenistan is the energy subsystem; however, water resources are the major factors in Uzbekistan. The introduced indicator enables a comparison of the WEF system between regions and temporal variations in a certain region. It can provide intuitive and effective data support for WEF nexus system management. [ABSTRACT FROM AUTHOR]