In the context of ecological protection and high-quality development strategy in the Yellow River Basin, green water management in the upper reaches of the basin is of great significance for conserving water sources, protecting fragile ecology and alleviating water shortage in the basin. There are many measures for green water management, and their effect needs to be further studied. An SWAT hydrological model was constructed in Huangshui Basin in the upper reaches of the Yellow River Basin. Five green water management measures, including contour tillage, residue mulching, stone line, terraced field and farmland conversion to forest on slops above 15° were simulated, and the changes of water quantity, sediment and water quality were analyzed. Combined with the coordination level of water, sand and quality management, the effects and applicability of different measures were explored. The results showed that farmland conversion to forest on slops above 15° had the best effect on increasing water yield and groundwater recharge, which were 1.77×107m3 and 1.72×107m3, respectively. Contour tillage and stone line can effectively regulate annual runoff distribution and reduce runoff in flood season. All the five measures can reduce the sediment yield load, among which terrace and stone line had the most significant effect, and the reduction rate was 13.5% and 13.0% respectively. All the five measures can reduce the total nitrogen (TN) and total phosphorus (TP) load, and the reduction rate in dry years was higher than that in wet years. The reduction effect of terraced and contour tillage was better, which was 24.6% and 14.7% for TN and 45.3% and 21.9% for TP, respectively. Through the water-sand-quality management collaborative analysis, excellent coupling can be achieved in the other four scenarios except for the residue mulching which was high coupling. The order of coupling coordination degree was terraced field, farmland conversion to forest on slopes above 15°, stone line, contour planting, residue mulching. The results can provide reference for green water management measures and optimal allocation of water resources in the Yellow River Basin.