Ecological environment quality reflects the overall condition and health of the environment. Analyzing the spatiotemporal dynamics and driving factors of ecological environment quality across large regions is crucial for environmental protection and policy-making. This study utilized the Google Earth Engine (GEE) platform to efficiently process large-scale remote sensing data and construct a multi-scale Remote Sensing Ecological Index (RSEI) based on Landsat and Sentinel data. This approach overcomes the limitations of traditional single-scale analyses, enabling a comprehensive assessment of ecological environment quality changes across provincial, municipal, and county levels in Fujian Province. Through the Mann–Kendall mutation test and Sen + Mann–Kendall trend analysis, the study identified significant change points in the RSEI for Fujian Province and revealed the temporal dynamics of ecological quality from 1987 to 2023. Additionally, Moran’s I statistic and Geodetector were employed to explore the spatial correlation and driving factors of ecological quality, with a particular focus on the complex interactions between natural factors. The results indicated that: (1) the integration of Landsat and Sentinel data significantly improved the accuracy of RSEI construction; (2) the RSEI showed a consistent upward trend across different scales, validating the effectiveness of the multi-scale analysis approach; (3) the ecological environment quality in Fujian Province experienced significant changes over the past 37 years, showing a trend of initial decline followed by recovery; (4) Moran’s I analysis demonstrated strong spatial clustering of ecological environment quality in Fujian Province, closely linked to human activities; and (5) the interaction between topography and natural factors had a significant impact on the spatial patterns of RSEI, especially in areas with complex terrain. This study not only provides new insights into the dynamic changes in ecological environment quality in Fujian Province over the past 37 years, but also offers a scientific basis for future environmental restoration and management strategies in coastal areas. By leveraging the efficient data processing capabilities of the GEE platform and constructing multi-scale RSEIs, this study significantly enhances the precision and depth of ecological quality assessment, providing robust technical support for long-term monitoring and policy-making in complex ecosystems.