Since the 21st century, there has been an influx of people into the coastal areas with the rapid urbanization process in China, and the trade activities of both coasts of the Taiwan Strait became more and more frequent, which led to ecological risks along the fragile seaboard. Therefore, it is important to dynamically monitor and evaluate the ecological quality of both coasts of the Taiwan Strait, which will promote ecological civilization construction and harmonious development across the Taiwan Strait. In this paper, Google Earth Engine platform was used to invoke the datasets of Landsat and MODIS from 2000 to 2022, based on which principal component analysis was adopted to construct the remote sensing-based ecological index. Then, difference analysis and spatial autocorrelation analysis were used to evaluate the eco-environmental quality differentiation of the Cross-Strait. In addition, the multi-ring buffer zones were established to study the effects of the size of main ports and city construction on the eco-environmental quality of the Cross-Strait. The results showed that: (1) from 2000 to 2010, the trend of eco-environmental quality was raised on the western coast and declined on the eastern coast of the Cross-Strait, and it was wavelike raised from 2010 to 2022 with the narrowing of the gap of the eco-environmental quality of the Cross-Strait. (2) The eastern coast's eco-environment was of higher quality than the western coast's. The eco-environmental quality level of Taimu Mountain and Yushan Mountain was excellent and good, and the relatively poor level was mainly in Huli District and Jinjiang City. Areas with significantly degraded eco-environmental quality levels were the mountainous regions on the eastern coast from 2000 to 2010, and the western coastal regions from 2010 to 2020. (3) There was a strong spatial correlation of the eco-environmental quality among cities on both coasts of the Strait, which showed that the remote sensing-based ecological index in the mountainous regions was higher and aggregated, while in the offshore regions was lower and aggregated. (4) On both coasts of the Strait, the effects of port size and its nearby urban construction on the eco-environmental quality were similar, showing that the eco-environmental quality was higher in areas farther away from the ports and where the proportion of urban construction was lesser. In the liner shipping stage, the eco-environmental quality around ports was worse when the port size was larger; the port size had a weaker impact on the eco-environmental quality which improved in the direct shipping stage. (5) Additionally, the eco-environmental quality of nearby ports slightly improved during the COVID-19 pandemic, and the ecological construction was taken seriously in Xiamen Port and Fuzhou Port. This study could provide basic data support for the construction of urban ecological civilization and a scientific decision-making basis for the plan of the ecological port, and could provide a boost to promote harmonious development on both coasts of the Taiwan Strait.