Energy, carbon, water and their interactions determine agricultural production efficiency and sustainability. On the Qinghai-Tibet Plateau (QTP), agricultural activities threaten the ecological security of the region, and agriculture itself is susceptible to climate change. In this study, we applied an energy-carbon-water nexus framework to assess the carbon emissions, water utilization, and energy flow, and their links with agricultural production on the QTP, using emergy analysis, footprint analysis (carbon footprint and water footprint) and a coupling model. The results showed that agricultural activities on the QTP released 2.17 × 1010 kgCO2-eq and absorbed 6.00 × 1010 kgCO2-eq, using 3.24 × 1022 sej of emergy and 8.19 × 109 m3 of water in 2018. Meanwhile, the energy-carbon-water nexus of agricultural production on the QTP was imbalanced, and the environmental footprint revealed large spatial heterogeneity at county scale. The coupling interaction among the energy-carbon-water nexus in agricultural production was investigated based on the coupling coordination model. Five categories of coupling interaction were identified by the degree of coordination. The largest emitter was agricultural input, especially electricity and nitrogen fertilizer, accounting for 24% and 7% of the total on average, respectively. With regard to emergy flows, renewable organic resources, accounted for 47%, making them the predominant in emergy inputs. The green water footprint (water from natural rainfall) at 51% was higher than the blue water footprint (water from irrigation) at 49%. More measurements to reduce carbon emission and improve the efficiency of energy usage and water usage are needed, such as optimizing planting patterns and structures, promoting cleaner energy, improving the efficiency of agrochemical use and proposing reasonable spatial planning for regional ecological development. Our findings provide a systematic reference for energy-carbon-water nexus analysis and sustainable agricultural development policy for decision-makers on the QTP.