In the context of pursuing high-quality development, the coupling and coordination of the ecosystem and economy has become the fundamental goal and inevitable choice for achieving the sustainable development of urban agglomerations. Based on remote sensing and statistical data for the Pearl River Delta (PRD) region from 2005 to 2020, in this paper, we construct an index system of the ecological and economic levels to assess the ecosystem service value (ESV). We use the equivalent factor method, entropy method, coupling coordination model, and relative development model to systematically grasp the spatial pattern of the levels of the two variables, analyse and evaluate their spatial and temporal coupling and coordination characteristics, and test the factors influencing their coupling and coordination using the geographical and temporal weighted regression (GTWR) model. The results show that ① the ESV in the PRD exhibited a fluctuating decreasing trend, while the level of the economy exhibited a fluctuating increasing trend; ② the coordination degree of the ESV and economy in the PRD exhibited a fluctuating increasing trend, and the region began to enter the basic coordination period in 2007; ③ in terms of the spatial distribution of the coordination degree, there was generally a circular pattern, with the Pearl River Estuary cities as the core and a decrease in the value towards the periphery; ④ the coordinated development model is divided into balanced development, economic guidance, and ESV guidance, among which balanced development is the major type; ⑤ the results of the GTWR reveal that the influencing factors exhibited significant spatial–temporal heterogeneity. Government intervention and openness were the dominant factors affecting the coordination, and the normalised difference vegetation index was the main negative influencing factor.