Abstract: Water scarcity, food crisis, and ecological degradation have been the bottlenecks in a considerable percentage of the world under the dual influence of global climate and human activities. Trade-offs between agricultural development and ecological effects are of great importance, especially in arid areas with highly developed agriculture. Water resources can be allocated, according to the mutual feedback relation among water, agriculture, and ecology. The agricultural and ecological water supply can also be optimized in different units. Synergy effects of the system can be expected to compromise the conflicts for the water security, sustainable development, and ecological health. In this study, an optimal allocation model of multi-water resources was constructed in the Shiyang River Basin using water-agriculture-ecology synergistic regulation. The objectives were taken as the groundwater balance, agricultural benefits, and ecological water use. Besides, the coordinated development degree was deduced using collaborative optimization with the NSGA-II algorithm. Trade-off and collaborative relationships were then quantified among water, agriculture, and ecology. The allocation schemes of water resources were finally proposed for the suitable water use proportion between agricultural and ecological under the synergistic promotion of water-agriculture-ecology. The results showed that the net water demand of irrigation was 14.99×10⁸ m³ in the Shiyang River Basin, whereas, the upper and lower water demand of ecological vegetation were 0.91×10⁸ and 3.35×10⁸ m³, respectively. The current balance between the supply and demand of water resources was attributed to the crowding out of ecological water and overexploiting groundwater. The water demand was also exceeded the water supply, in order to fully meet the minimum demand of for ecological water and groundwater. There was a water shortage of 1.44×10⁸-2.93×10⁸ m³/a in the Liuhe subsystem alone. Furthermore, the agricultural benefits, ecological water use, and groundwater balance were 137.53×10⁸ Yuan, 0.60, and 0.59×10⁸ m³, respectively, in the optimal allocation scheme. The agricultural benefits increased by 1.9% than before. The positive balance of groundwater was achieved in 0.59×10⁸m³. The agricultural and ecological water was accounted by for 90% and 10%, respectively, in the whole watershed, while that in canals and wells was 67% and 33%, respectively. The economic benefits of schemes S2 and S4 were reduced by 5.4%, compared with the optimal decision scheme (S0), while the groundwater balance of schemes S1 and S3 was reduced by 92.9% and 95.2%, respectively. Compared with the baseline, there was a 6% reduction in the water diversion from the middle reaches under diverse water and soil resource management, in order to guarantee a water inflow of 3.48×10⁸m³/a from Caiqi. In this case, the agricultural and ecological water consumptions of the Liuhe subsystem were 13.87×10⁸ and 1.62×10⁸m³, respectively, while the groundwater was in a positive equilibrium of 0.70×10⁸m³. When the inflow in Caiqi was 3.48×10⁸m³/a in a normal year, the ecological water use and groundwater were achieved to balance 1.6% of the agricultural benefits in the middle reaches. The ecological water use and the balance of groundwater were elevated by 4.8% and 18.6%, respectively, compared with the baseline. There was a synergistic trade-off between groundwater balance and ecological water in agriculture. The water resources in arid areas can be managed to maintain an appropriate balance among water security, agricultural development, and ecological health. Failure to consider the mutual influence among different water users can result in the decision biases and suboptimal schemes. This finding can provide an effective way to analyze the complex relationship among water, agriculture, and ecology. A strong reference was also offered for water resource planning and management in arid basins.