Chongqing is a large municipality in southwestern China, having the characteristics of a vast jurisdiction, complex topography, and a prominent dual urban–rural structure. It is vitally important to optimize the spatial layout of land and efficiency of natural resource allocation, achieve sustainable development, and conduct influence assessment and causation analysis in this region. Here, using the Google Earth Engine platform, we selected Landsat remote-sensing (RS) images from the period 2000–2020 and constructed a remote-sensing ecological index (RSEI) model. Considering the urban spatial pattern division in Chongqing, the Sen + Mann–Kendall analytical approach was employed to assess the fluctuating quality of the ecological environment in different sectors of Chongqing. Subsequently, single-factor and interaction detectors in the Geodetector software tool were used to conduct causation analysis on the RSEI, with the use of eight elements: elevation, slope, aspect, precipitation, temperature, population, land use, and nighttime lighting. Findings indicate that, over the course of the investigation period, the eco-quality in Chongqing displayed a pattern of degradation, succeeded by amelioration. The RSEI decreased from 0.700 in 2000 to 0.590 in 2007, and then gradually recovered to 0.716 in 2018. Overall, the eco-environment quality of Chongqing improved. Spatially, changes in the RSEI were consistent with the planning and positioning of the urban spatial pattern. The main new urban area and periphery of the central urban area showed a slight deterioration, while other regions showed marked improvement. The combined effect of any two elements enhanced the explanatory power of a single factor, with elevation, temperature, and land use being the strongest explanatory elements of eco-quality in Chongqing. The most influential factor explaining the spatial variation of the RSEI was determined to be the combined impact of elevation and land use. At the temporal scale, elements related to human activities showed the most evident trend in explanatory power.