In the process of developing the world-class bay area and urban agglomeration in the Guangdong-Hong Kong-Macao (GHM) Greater Bay Area, ecological protection and environmental optimization are equally important with urban development and economic openness. Understanding the changes in ecosystem services during the urbanization process of the GHM Greater Bay Area will help policymakers formulate scientific, rational, and targeted policies on ecological protection. Based on the macro-ecosystem changes in the GHM Greater Bay Area from 2000 to 2015, this paper analyzes the spatial and temporal evolution characteristics of ecosystem productivity, water conservation, and soil conservation services in the GHM Greater Bay Area during the past 15 years, and discusses the relationship of trade-offs and synergies between supply and regulation services. The results show that: (1) forests and farmlands are the main ecosystems of the GHM Greater Bay Area, accounting for 54.1% and 22.8% of the land area. Due to the rapid expansion of the urban area (increase of 68.6% from 2000 to 2015), the areas of forests, farmlands, and wetlands have continued to decrease in the past 15 years. (2) The ecosystem supply services (based on Net Primary Productivity, NPP) and soil conservation show a slight increase, especially the main service supply areas in Jiangmen and Zhaoqing of the GHM Greater Bay Area. The water conservation reaches its highest along the southeast coast, and followed by the northern region, while the central region of the GHM Greater Bay Area is relatively lower. Except for the increasing trend observed in the northwest region, other regions are showing a decreasing trend in water conservation. Urban expansion is the main influencing factor for the apparent reduction of ecosystem services. (3) The correlation between ecosystem services and water and soil conservation services in the GHM Greater Bay Area mainly shows a synergy, while the relationship is mainly a trade-off in south and northeast of the GHM Greater Bay Area (Guangzhou, Huizhou and Jiangmen). It is suggested that during the development of the GHM Greater Bay Area, special attentions should be paid to the targeted ecological protection measurements in areas where the supply and regulation services are trade-offs. Relevant departments need to implement a strict ecological environment protection system, and adopt measures such as optimizing the structure of green space and protecting ecological space to reduce the negative impact of urban expansion and unreasonable human activities on ecosystem services, and build the Greater Bay Area with a beautiful ecological environment and cultural prosperity.