The Zhongyuan Urban Agglomeration functions as a strategic spatial platform driving sustainable development in the Yellow River Basin. A scientific understanding of the spatiotemporal differentiation characteristics and formation mechanisms of hydro-ecological space evolution within this region is essential to support water ecological space use regulation and integration into the national territorial spatial planning system in the lower Yellow River area. This study employs a space-time cube model to characterize the interannual dynamics and typical patterns of hydro-ecological space within Zhongyuan Urban Agglomeration from 2000 to 2023. A comprehensive analysis of spatial structure transformation is conducted from two critical dimensions-scale and location-to systematically capture the extent, spatial distribution, and dynamic shifts of hydro-ecological space within the Zhongyuan Urban Agglomeration. This analysis enables a refined understanding of spatial configuration changes, expansion-contraction dynamics, and regional structural adjustments over time. To further investigate the underlying drivers of these transformations, the study employs a Mantel test matrix to quantitatively examine the correlation between hydro-ecological spatial structure evolution and a range of potential influencing factors, including natural geographic attributes, socioeconomic conditions, and infrastructural developments. By assessing the strength and significance of these spatial associations, the study identifies key determinants shaping hydro-ecological space changes. Building upon this foundation, an XGBoost model is integrated with an interpretable machine learning framework, VIVI-PDP, to conduct an in-depth exploration of the evolution mechanisms. This approach allows for a precise evaluation of factor importance, the strength of interactions among key variables, and the complex nonlinear dependencies influencing hydro-ecological space transformation.The results reveal that: ①Over the past 23 years, hydro-ecological space expanded by 805.53 km² (33.52% growth rate), exhibiting a phased evolutionary trajectory: expansion→stabilization→expansion→stabilization, demonstrating cumulative ecological resilience. ②The dynamic conversion between "agricultural space-hydro-ecological space" is particularly pronounced, with significant differences across the six functional zones of the urban agglomeration. Notably, hydro-ecological space transformation is most active in high-efficiency ecological demonstration zones, relatively active in core development and cross-regional coordinated development areas, and less pronounced in transformation and innovation development areas and industrial transfer zones. High-intensity transition clusters (HH-type) predominantly occur in resource-rich western/southern/eastern zones, while low-low clustering (LL-type) areas are mainly located in the northern and central areas, where both the influx and outflux of hydro-ecological space are relatively limited. ③Natural geographic conditions and transportation location are the primary driving factors in the dynamic transformation of hydro-ecological space. However, during the transition from hydro-ecological space to agricultural space and from urban space to hydro-ecological space, socioeconomic drivers emerge as dominant determinants. The interplay of natural and human factors results in a transformation process manifesting multifactorial synergies with pronounced spatial heterogeneity.