The development of urban agglomerations are generally accompanied by the optimization and upgrading of industrial structure, population transfer and quality improvement, and the improvement and deepening of innovation capabilities. The Guangdong-Hong Kong-Macao Greater Bay Area has attracted worldwide attention as the new engine of China's economy and an important growth pole that promotes global economic development. Based on the three key elements of industry, population, and innovation, this paper takes the Greater Bay Area as the research area, relying on the theory of the function upgrade of the key elements of urban agglomeration development, selects representative index of the level of industrial clusters, population mobility, and technological innovation support, uses quantitative measurement, statistical description, and qualitative analysis methods to analyze the current functional status and existing problems of key elements in the study area. At the industrial level, the service-oriented economy has a characteristic of agglomeration, but the degree of advanced industrial clusters is not enough. The Guangdong-Hong Kong-Macao Greater Bay Area has not yet formed a number of high-end industrial clusters with distinctive regional characteristics and outstanding international competitiveness, including high-end producer services, high-tech manufacturing, and strategic emerging industries. At the demographic level, the Greater Bay Area has strong attractiveness, but the degree of talent concentration, high-end and internationalization is low and far below international standards. At the innovation level, the Greater Bay Area has a certain foundation and vitality for science and technology innovation, but the original innovation capabilities are insufficient. Especially, the relative lack of cutting-edge talents is also a constraint to the original highland creation in this region. In response to the existing problems, we propose a path to upgrade the functions of key elements such as the cultivation of high-end manufacturing and producer services, the enhancement of talent gathering functions, the improvement of talent flow guarantee mechanism, and the enhancement of original innovation capabilities. The suggestions in the paper should promote the further optimized development of the Greater Bay Area and provide certain decision-making reference for enhancing the influence and competitiveness of the bay areas in global economy.