Owing to the development issues of the Guangdong-Hong Kong-Macao Greater Bay Area in the new domestic and international situation, the content, challenges, and paths of innovation and development of the Greater Bay Area are explored from multiple dimensions, including economic, social, cultural, and institutional. The innovation and development of the Greater Bay Area should strengthen technological and industrial innovation capabilities, improve regional resilience to cope with external shocks, increase the mobility of intraregional factors, improve the well-being of the people's livelihood, enhance the capacity of spatial governance, promote integrated urban-rural development, and optimize the regional pattern of ecological security. The conclusion is that considering the innovation and development of the Greater Bay Area from a systemic and interconnected perspective is crucial for seeking innovations in various development fields and promoting coupling and coordination among them. Therefore, the region may acquire the agency that can continuously break through bottlenecks, resolve external shocks, and unlock new paths of development. We call for the strengthening of cross-field and cross-disciplinary collaborative research to contribute the power of geography to the realization of the development goals of the Guangdong-Hong Kong-Macao Greater Bay Area.