Display omitted •A framework for assessing coordinative relationship was established.•Coordinative relationship was quantified by using coupling coordinating degree model.•The CES of each city in ARDUA had deteriorated during the study period.•The coordinative relationship in ARDUA was always in a state of mild incoordination.•The coordinative relationship showed an obvious regional difference. Understanding the coordinative relationship between urbanization and ecosystem services (ESs) has a great significance in sustainable development in urban agglomeration. In this paper, InVEST model was firstly used to assess the spatio-temporal evaluation of four types of ESs (water yield, carbon storage, soil retention and nitrogen export) in the Yangtze River Delta Urban Agglomerations (YRDUA) of China from 2000 to 2020. Then comprehensive evaluation index system of urbanization was established from the multi-dimensions of economy, population and land to analyze the urbanization level during the study period. Finally, a comprehensive ecosystem service (CES) index was developed to explore the coordinative relationship between ESs and urbanization by using coupling coordinating degree model (CCDM). The results revealed that: 1) Urbanization has led to greatly land use/ land cover change, which caused the degradation of carbon storage and water purification, and the improvement of water yield and soil retention. The higher water yield and nitrogen export mainly clustered around urban areas, while higher carbon storage and soil retention were distributed in forest-rich cities in the Zhejiang and the southern of Anhui. There were positive correlations between different ESs. And the CES of cities in the YRDUA had deteriorated during the study period. 2) The urbanization levels of almost all cities showed an overall upward trend, with Shanghai the highest urbanization, followed by Nanjing and Hangzhou, and rapid urban expansion mainly occurred in developed urban areas. 3) The coordinative relationship between CES and urbanization in the YRDUA was always in mild incoordination, showing an obvious spatial distribution pattern of “higher in the south, but lower in the north”. The coordinative relationship between CES and urbanization in most cities in the north of YRDUA has not achieved coordination development, with the state of moderate or mild incoordination, while the cities in the south has attained coordination development, with the state of primary or even superior coordination. Therefore, our study suggested that differentiated urban space management and control policies should be made for the YRDUA to improve the overall coordinative relationship between CES and urbanization.