Based on the construction of the evaluation index system of high-quality development of green economy and digital economy, two-way fixed effect model and intermediary effect model were adopted to analyze the mechanism of digital economy in Guangdong-Hong Kong-Macao Greater Bay Area on high-quality development of green economy. Digital economy can effectively improve the high-quality development level of green economy, and regional heterogeneity analysis shows that the central city is more significant. The digital economy further improves the level of high-quality development of the green economy through low-carbon technological innovation and human resources reserve. It is concluded that the consolidation and construction of the digital economy in the Guangdong-Hong Kong-Macao Greater Bay Area is still of great significance, and internal differences should be reduced to form a green and sustainable development path.