Economic globalization and rapid urbanization have affected ecological environments in global regions to different degrees. Timely, objective and quantitative evaluations of the spatiotemporal variations in regional ecological environmental quality are the key to environmental protection and decision making. The spatial distributions of ecological environment quality levels along the Jakarta–Bandung high-speed railway from 2000 to 2020 were obtained based on Google Earth Engine and the Remote Sensing Ecological Index (RSEI). Then, the Theil–Sen median and Mann-Kendall methods were used to assess the temporal RSEI trend; the spatial autocorrelation evaluation index was used to evaluate RSEI clustering on a spatial scale. The results show that the overall ecological environmental quality from 2000 to 2020 was moderate, with temporally fluctuating changes and very significant spatial clustering. Approximately 20% of the area showed very strong changes (improvement or degradation). Areas with relatively better ecological quality were located mainly in relatively high-elevation and high-vegetation-coverage regions, while areas with poorer ecological quality were located mainly in the four major cities, including Jakarta, with concentrated populations and developed economies. The research results provide local governments with scientific suggestions regarding the synergistic development of high-speed railway construction and ecological environmental protection.