Rapid urbanization induces negative impact on ecosystem services (ESs). Scientific identification of the spatial distribution and management of ESs is of great significance to sustainable development of land and resource. Currently, the lack of research on meso and micro scale limits further cognition of ESs. Additionally, homogeneous urbanization was generally taken as the premise to analyze the evolution characteristics of ESs by former research, which cannot meet the needs of fine land management. Based on land use, remote sensing, point of interest and other data, this paper analyzed the spatial distribution and trade-off/synergy relationship of six ESs in Xiamen, using ArcGIS and InVEST platform. Moreover, artificial neural network algorithm and land development assessing model were introduced to quantitatively identify the spatial pattern of urbanization. Finally, spatial management strategies were proposed through decision matrix. The results showed that (1) the distribution of ESs in Xiamen was significantly different on the land-sea direction. The four off-island districts of Xiamen contributed to 91.78% of the comprehensive ecosystem service (CES) in the study region. The total amount and average level of CES in Tong'an District were both the highest. (2) There were mainly synergistic effects between the ESs in Xiamen. From the perspective of overall relationship, habitat quality and runoff mitigation, habitat quality and temperature mitigation both showed high synergy. From the perspective of local spatial relationship, the synergy level of water conservation and flood regulation was the highest, while the trade-off effects between recreation service and other ESs were very significant. (3) Through identification of urbanization characteristics, Xiang'an District showed highest developing potential, and Tong'an District showed high level of over-urbanization. After spatial subdivision and classification, it was found that the service levels of habitat quality, water conservation and runoff mitigation were higher in the non-development units, and the built-up units only got an advantage on recreation service level. (4) Integrating spatial characteristics of urbanization and ESs distribution, the ecological control zoning map of Xiamen was put forward, based on the spatial subdivision units. Furthermore, the specific management strategies of four types of units in eight scenarios were proposed through the decision matrix. Sustainable development is to find a balance between ecological protection and economic development, so as to maximize the comprehensive benefits. Through the identification of the complex spatial relationship between ESs and the interaction between CES and urbanization process, this paper provides quantitative decision support for the fine management and control of urban ecological space.