In the context of urbanization in Northwest China, the tension between the management of water resources and the allocation of green space has become increasingly evident, primarily manifesting as “water-green misalignment” and “water-green mismatch”. Current research predominantly focuses on the horizontal aspects of water-green co-location, emphasizing the water-retention function of green spaces. In contrast, investigations into how water improves habitat conditions and how vegetation adapts to water availability remain comparatively limited, leaving considerable room for further in-depth exploration and refinement. This study broadens the concept of “green” to encompass the vertical dimension, underscoring the multi-layered role of vegetation in water resource adaptation and ecological functionality. It proposes a theoretical model of “water-green co-location” along with an ecological design approach that integrates spatial layout and vertical structure. This approach was implemented in the design practice at Fengxi New City Innovation Port Middle School, showcasing certain ecological and economic benefits while further substantiating the feasibility and necessity of establishing a horizontally and vertically coordinated water-green co-location mechanism.