Ecological environment is closely related to the development of society and economy. Analyzing the process of ecological environment evolution is of great significance for guiding regional ecological environmental protection. However, analysis of regional ecological environment evolution based on a single indicator such as surface water area, groundwater level, normalized difference vegetation index (NDVI), etc., has limitation in a single perspective. Taking the Minqin Basin in the lower reaches of the Shiyang River as the study area. Firstly, spatial and temporal changes of four indicators, including surface water area and storage of Qingtu Lake, the terminal lake of the Shiyang River, groundwater level and storage anomaly, land use, and NDVI in Minqin Basin were analyzed. Then a comprehensive analysis of ecological environment evolution was conducted for the Minqin Basin from multiple perspectives, including surface and groundwater resource variations, land use type changes, and NDVI dynamics. The results shown that the water surface area and storage of Qingtu Lake generally followed a trend of drying up, increasing and shrinking. The groundwater water level and storage anomaly in the Minqin Basin generally showed a downward trend, with a significant slowdown in the decline from 2007 to 2013. The changes in land use types in the Minqin Basin were mainly characterized by the conversion between cropland, grassland, and barren, and since 2017, desertification in the Minqin Basin intensified. The NDVI in the Minqin Basin showed a non-significant increasing trend with a rate of 0.0005a-1. By integrating the characteristics of the changes of surface water and groundwater resources conditions, land use types, and NDVI changes, the process of the ecological environment evolution in the Minqin Basin from 2003 to 2022 was divided into three stages of rapid degradation (2003—2006), recovery (2007—2013), and re-degradation (2014—2022) based on multi-perspective. Changes of water resources conditions induced by human activities constituted the primary factor influencing ecological evolution in the Minqin Basin. Establishing a regional economic and social development model that was coordinated with and compatible to the water resource carrying capacity of the Minqin Basin should be prioritized as a key direction for ecological conservation in the region.