The Guangdong-Hong Kong-Macao Greater Bay Area has become the most important national strategic zone in China because of its key engine-like role for economic growth as well as being the most advanced global mega-city region in China. The mega-city region development is based on reasonable labor division and cooperation between cities. Cities should focus on their strengths and boost regular competition to promote the coordinated development of the entire region. This study examines the Guangdong-Hong Kong-Macao Greater Bay Area, which includes 19 national economic industries that are divided into 11 city functional types. Based on the data concerning the industry practitioners in each city in 2003 and 2017, this study uses the location quotient index, urban basic service scale measurement method, and Nelson urban functional intensity index to analyze the dynamic evolution of city functions in 2003 and 2017 from the perspective of three elements of urban functions. Further, the influence factors of evolution are analyzed according to the economic, political, and social aspects. First, the urban agglomeration of the Guangdong-Hong Kong-Macao Greater Bay Area is dominated by the manufacturing and production services, with a high specialization level being observed for the manufacturing and service functions, and the evolution of these functions exhibits obvious spatial heterogeneity and industry differences. Second, at the regional level, the basic functions of the Guangdong-Hong Kong-Macao Greater Bay Area include the manufacturing industry, commerce, real estate industry, leasing business services, and software information services, whereas the non-basic functions include transportation, finance, scientific research and technology, education, culture and health, and other services and industrial functions. The functions of the service industry are observed to be significantly enhanced from 2003 to 2017. Third, at the city-scale level, the urban functions of the Greater Bay Area are primarily undertaken by the four major central cities of Hong Kong, Macao, Guangzhou, and Shenzhen, with uneven development being observed between the central and peripheral cities. However, the status of the manufacturing function in central cities declined with the rapid growth of the producer service functions and high specialization levels. In particular, Guangzhou and Shenzhen, which are two core cities in the Pearl River delta, have rapidly improved their functional status and exhibit comparatively increasing advantages with respect to transportation, software information, leasing businesses, and scientific research and technology, challenging the functional status of Hong Kong and Macao. However, the remaining node cities are dominated by the manufacturing functions, and their service functions exhibit a relatively low level of specialization. Foshan, Dongguan, Zhongshan, and Huizhou are cities that dominate with respect to the manufacturing industries, whereas Zhuhai exhibits a relatively good service function development and can build a sub-center of services in the bay area. Jiangmen and Zhaoqing have improved their functions; however, their urban influences and strengths are weak. Fourth, the evolution of urban functions in the Guangdong-Hong Kong-Macao Greater Bay Area is primarily influenced by the urban location conditions, the economic development level, the regional development policies and strategies, the economic globalization, and the most recent round of technological revolutions. In the future, policymakers and planners should focus on achieving a reasonable division of the urban landscape by relying on information technology to promote the development of the integration of manufacturing and services, promoting the transformation and upgradation of industries, and accelerating the regional system innovation and cooperation to achieve high-quality integrated development in the Guangdong-Hong Kong-Macao Greater Bay Area.