At present, Zhuhai and Macao have room for cooperation in the development of green finance, and both sides should seize the opportunity to achieve shared and synergistic development. There is a basis for regional cooperation in the development of green financial markets in the Guangdong-Hong Kong-Macao Greater Bay Area, and the “9 + 2” city clusters in the Greater Bay Area have all laid out their green financial policies and systems accordingly, and have begun to yield results. However, for Guangdong, Hong Kong, and Macao, there exist problems such as different green financial legal systems, lack of green financial information sharing platforms, and inconsistent implementation standards. Considering the differences in the positioning of green finance functions between Macao and Hengqin, we suggest that Macao and Hengqin can make a breakthrough in their cooperation in the development of green finance by encouraging the issuance of green bonds and green securities products and experimenting with green lottery and green financial derivatives.