• A novel optimization approach for agricultural water-food-energy nexus is developed. • Electricity, bioenergy and light energy are modeled, optimized and coordinated. • Dynamics and uncertainties in the nexus are simultaneously managed. • Conflicts between multiple energy sources and various resources are balanced. • Nexus sustainability and resource/energy use efficiency are improved. Synergistic regulation of various agricultural resources in agricultural water-energy-food nexus systems is important for understanding the key regulatory processes and related synergistic relationships. However, regulation with the goal of multienergy interaction and coordination to adapt to environmental changes is extremely challenging. As a solution to the problem, an uncertainty-based modeling approach is proposed for the optimal regulation of water, soil and energy resources from a multienergy synergy perspective by integrating multiobjective nonlinear programming, left–right type fuzzy numbers and credibility programming into a framework. The approach aims to assess the interactions and synergistic relationships among biomass electrical energy, light energy, and hydroelectric energy, clarify the dynamic characteristics of resource allocation and socioeconomic and environmental effects, and capture the high uncertainty in the nexus area. This study contributes to the efficient and sustainable management of agricultural water, energy and land resources. The approach was tested and implemented based on a case study of Jinxi Irrigation District in China. The results reveal that there are trade-offs and games among the light use efficiency, hydroelectric energy and biomass energy, and their coordination enhances the system synergy among resources, the economy and the environment by 12.22%, with a 2.67% increase in the irrigation water use efficiency and a 4.92% increase in the energy use efficiency. Uncertainties significantly affect the synergy among multiple energies. More water will promote collaborative energy management, w...