Agroforestry systems are widely promoted for their economic and environmental benefits. Food, energy, water and land resources in agroforestry systems are inextricably intertwined and expected to be severely impacted by climate change. Socioeconomic development and increasing populations have posed unique challenges for meeting the demand for food, energy, water and land, and the challenge will become more pressing under projected resource shortages and eco-environmental deterioration. Thus, a method of optimizing and sustainably managing the water-land-food-energy nexus in agroforestry systems under climate change must be developed.This paper develops an optimization model framework for the sustainable management of limited water-land-food-energy resources in agroforestry systems under climate change. The aims are to (1) quantify the interactions and feedbacks within water, land, food and energy subsystems; (2) provide trade-offs among water and energy utilization efficiency, economic benefits and environmental protection in agroforestry systems; and (3) generate optimal policy options among water and land resources for different crops and woodlands in different regions under different climate change patterns.The model framework is based on multiobjective fractional programming, and compromise programming is used to solve it. Climate change patterns are obtained from atmospheric circulation models and representative concentration pathways. The above aims are investigated through an actual nexus management problem in northeast China. Spatiotemporal meteorological and report-based databases, life cycle assessments, Pearson correlation analyses, data envelopment analyses and analytic hierarchy processes are integrated to realize practical application.The results show that climate variation will change the water and land allocation patterns and these changes will be more pronounced for major grain-producing areas. The optimized water allocation decreased (especially for rice, e.g., the optimal average value of the irrigation quota of rice was 4226 m³/ha, while the corresponding actual irrigation requirement of rice was [4200–7200] m³/ha) to improve the water use efficiency, and surface water allocation accounted for two-thirds. Maize had the largest planting area, although planting soybean generated the most greenhouse gases (greenhouse gas emissions from field activities for rice, maize, and soybean were 43.46%, 84.06% and 91.16%, respectively); However, these gases can be absorbed by forests. The model improved the harmonious degree of the resource-economy-environment system from 0.24 to 0.56 after optimization.Integrated models contribute to the sustainable management of water, food, energy and land resources and can consider the complex dynamics under climate change. It can be used as a general model and extended to other agroforestry systems that show inefficient agricultural production.