Water scarcity, land pollution, and global warming are serious challenges and crises facing the development of sustainable or green agriculture and need to be addressed using efficient and environmentally friendly management strategies. This paper proposed an integrated framework appropriate for agricultural green total factor productivity (AGTFP) assessment coupled with microscopic and mesoscopic perspectives under water-energy-food (WEF) nexus, which generated scientific and reasonable strategies for green and low-carbon agriculture from internal core factors and peripheral environmental impacts to improve green agricultural production sustainability. Taking the Lianshui irrigation district (LID) with three sub-areas as the object, internal core factors were explored by partial least squares regression (PLSR) and the external impact path through partial least squares structural equation modeling (PLS-SEM). Results indicated that AGTFP in LID was the smallest (0.818) compared to the three sub-areas and was in a fluctuating state. Meanwhile, AGTFP which was calculated considering undesirable outputs, was closer to tangible productivity. Resource endowments and technical facilities will promote agricultural production, desirable outputs will stimulate green production, and undesirable outputs can inhibit green production. The external influence pathway was shown to be primary environment - > secondary environment - > economic aspects - > social aspects - > AGTFP. The innovative perspectives presented in this study can facilitate preferable decisions and avoid unintended consequences for human-natural systems. Display omitted •Established agricultural green total factor productivity (AGTFP) to enhance green production sustainability•The integrated framework amalgamating core with peripheral water-energy-food nexus was constructed.•The slack-based measure directional distance function including undesirable outputs was closely aligned with tangible productivity.•The manipulation of internal input indicators demonstrated superior efficacy compared to output indicators.•The AGTFP was predominantly influenced by the primary and secondary environmental determinants.