As an open place for residents to relax and get close to nature, ecological recreation space (ERS) plays an important role in improving residents’ life quality and wellbeing. With the integrated development of urban agglomerations and the increasingly high requirements of urban residents for the quality of their habitat and leisure environment, the regional organization of recreational use of ecological space within urban agglomerations has become a new hot topic. Based on the definition and spatial interpretation of ERS, this paper analyzed the spatial agglomeration and differentiation characteristics of ERSs in the Pearl River Delta urban agglomeration (PRDUA) by using GIS spatial analysis methods. The spatial relationship between ERS and other humanities and natural ecological elements were also analyzed to reveal the problems and causes of the distribution of ERS. The results show that: (1) The spatial differentiation of recreational utilization rate of ecological space in each city is obvious, which reflects the lack of effective regional co-ordination of recreational utilization of ecological space. (2) The distribution of ERS’s number, scale, grade, and recreational utilization rate of ecological space is characterized by spatial agglomeration, but with different agglomeration orientations. (3) The distribution of ERS is spatially dependent on topography and traffic, but its link with the distribution of water systems, tourism elements, and cultural resources is not evident. (4) The area distribution of ERS is opposite to that of population density, suggesting the contradiction between the supply and demand of recreation services of ecological spaces. Compared with previous studies, this study attempted to reveal more factors that affect the spatial distribution of ERS in regional scale through the empirical study in PRDUA. It can be concluded that the factors affecting the spatial differentiation of ERS include three natural factors, i.e. topography, water system, and ecological space distribution, and three human factors, i.e. population density, transportation and regional policy and management. Interestingly, ERS distribution is not significantly correlated with the tourism elements and cultural resources, which suggests that the coordination between ERS layout and tourism and cultural system needs to be improved in the future in PRDUA.