Maintaining an optimal eco-environment is important for sustainable regional development. However, existing methods are inadequate for examining both spatial and temporal dimensions. Here, we propose a systematic procedure for spatiotemporal examination of the eco-environment using the space-time cube (STC) model and describe a preliminary investigation of the coupling relationships between basin ecological quality and water eutrophication in upstream of the Han River basin between 2000 and 2020. The STC model considers the temporal dimension as the third dimension in calculations. We first categorized the basin into three sub-watershed types: forest, cultivated land, and artificial surface. Subsequently, the ecological quality and driving factors were assessed and identified using the remote sensing ecological index (RSEI) and Geodetector method, respectively. The findings indicated that the forest basin and artificial surface basin had the highest and lowest ecological quality, respectively. The spatiotemporal cold spots of ecological quality during the past 20 years were mostly located in the vicinity of reservoirs, rivers, and artificial surface areas. Human activity, precipitation, and the percentage of cultivated land were other important driving factors in the artificial surface, forest, and cultivated land sub-watersheds, respectively, in addition to the dominant factors of elevation and temperature. The results also indicated that when the ecological quality degraded to a certain extent, water eutrophication was significantly coupled with the ecological quality of the catchments. The findings of this study are useful for ecological restoration and sustainable river basin development.