Propelled by the ongoing global technological revolution and industrial transformation, the digital economy has emerged as a pivotal driver of economic growth, reshaping industries and global markets. Leveraging its distinct geographical advantages, the Guangdong-Hong Kong-Macao Greater Bay Area (GBA) has rapidly positioned itself as a leader in digital economy development, fostering innovation and attracting investments. This study applies both the coupling coordination degree model and the obstacle degree model to systematically analyze the spatial-temporal patterns, as well as the key influencing factors, of the coupling coordination between the digital economy and high-quality economic development in the GBA over the period from 2011 to 2021. The results indicate that, with Guangzhou and Shenzhen at the core, the GBA has experienced steady growth and a marked improvement in coordination. However, significant regional disparities in coordination remain, indicating the need for further strategic integration. Finally, the study employs the obstacle degree model to pinpoint the critical factors affecting coordination, offering targeted policy recommendations to overcome these challenges and further promote the development of the GBA, ultimately contributing to the region’s long-term, sustainable growth and global competitiveness.