Based on the water footprint method, the water scarcity in the Yellow River Basin is evaluated from a comprehensive perspective of water quantity-water quality-ecology water demand. The results showed that the blue water footprint and grey water footprint of the Yellow River Basin are 52.65 billion and 305.62 billion m³, respectively. When only considered water quantity and ecology water, the water scarcity pressure of the Yellow River Basin is low, of which 85.4% of the cities are under low water scarcity pressure and only 10.1% are under extreme water pressure. After incorporating water quality factors, only 15.7% of the cities are under low water scarcity pressure, and 64.0% are under extreme water pressure. Water quality has greatly exacerbated the water scarcity in the basin. It is suggested to jointly promote water resources management and protection, and to facilitate water-saving technologies and water recycling. Efforts should focus on improving agricultural water use efficiency and strengthening pollution control to alleviate the conflict between economic development and water constraints in the Yellow River Basin.