With the rapid development of urban agglomerations in the Pearl River Estuary (PRE), an increasing number of ecological problems have been exposed to the surrounding coastal zones. The timely and accurate understanding of the eco-environment in PRE has become of increasing concern. This study aimed to quantitatively evaluate multi-temporal eco-environment conditions and then detect the conflicting patterns of the eco-environment under the influence of coastal exploitation in PRE. The ecological index was derived from remote sensing images by means of principal component analysis, and the composite coastal development index was then constructed to characterize the coastal exploitation from the perspective of ecological influence, which was implemented by using the panel data analysis. This method was verified with a significant test accuracy of 0.9. Based on this, the coupling coordination patterns of the coastal economy–environment system were disclosed for all six prefectural units at both the pixel scale and the city scale. The results showed that the coupling coordination degree and inner coupling relationships in each city presented periodical characteristics, with the highest values in 2008 and the lowest values in 1988. The dominant conflict between coastal exploitation and the eco-environment in each period was capricious. This evaluation will provide a reference for decision-making in coastal zone planning and ecological red line policy to encourage the sustainable development of coastal zones.