CONTEXT: Synergies between water-energy-food-ecology (WEFE) nexus essentially embody the sound functioning of complex adaptive systems. As an effective way of promoting the transformation of agricultural systems, it is critical to compare the synergies between conventional and organic farming systems from a nexus perspective, and to explore the contribution of synergies to achieving sustainable development in agriculture. OBJECTIVE: This study aims to develop an integrated framework to facilitate assessment of the complex dynamics and potential for coordinated development of the WEFE nexus under organic and conventional farming. We also try to explore the relationship between system synergies and gross ecosystem product values, identifying key factors that influence systematic synergy. METHODS: In this study, we developed a comprehensive WEFE nexus evaluation index and applied it to a case study of the tea industry in Simao District, Pu'er City, Yunnan Province, China. We employed the coupled coordination degree (CCD) model and Pearson's correlation coefficient to compare the synergies between organic and conventional farming systems. Regression analysis and the co-effect gradation index were used to investigate the relationship between system synergy and gross ecosystem product values. Additionally, the random forest method was applied to identify factors dominating the synergies of the WEFE nexus, providing strategic directions for system optimization. RESULTS AND CONCLUSIONS: The results show that the sustainable development index and the degree of coordination of the organic tea farming system were 72.41 % and 53.40 % higher, respectively, than those of the conventional tea farming system. Hence, the organic tea farming system displayed clear advantages in terms of enhancing its synergy related to sustainability. Furthermore, the synergies of WEFE nexus were significantly positively correlated with the gross ecosystem product values (GEPV), and a 0.1 enhancement in the CCD of the organic farming is associated with an increase of approximately 4130 CNY of GEPV, which is 2.6 times the marginal benefit of conventional farming. We also find that the ecology and energy subsystems play dominant roles in influencing synergy, and thus improving ecosystem services and energy efficiency can be seen as key strategies for promoting multidimensional coordination. SIGNIFICANCE: This study demonstrates the feasibility of applying the nexus concept to sustainable development in agriculture, illustrating the potential of organic farming for coordinated growth and the substantial benefits that can generated through synergistic optimization of integrated systems. Therefore, enhancing synergies of WEFE nexus can offer valuable insights for advancing the sustainable development of agricultural systems.