The Guangdong-Hong Kong-Macao Greater Bay Area is an important strategy for regional development in the 14th Five-Year Plan, which puts forward higher requirements for the quality of talent cultivation. Whether the educational structure of graduate students is reasonable and whether there are sufficient and reasonable high-level talents with knowledge and skills structure is the key to support the development and construction of the Guangdong-Hong Kong-Macao Greater Bay Area. The San Francisco Bay Area, as the first region in the world to build a “Bay Area”, has a prominent influence in the fields of education, economy, science and technology in the world, and the optimization and adjustment of postgraduate education structure has important reference significance for the Guangdong-Hong Kong- Macao Bay Area with the same orientation. This paper puts forward the optimization strategy of structure of graduate education to meet the economic development level and future development needs of the Guangdong-Hong Kong-Macao Greater Bay Area based on the analysis of the San Francisco Bay Area: Graduate education in the Guangdong-Hong Kong-Macao Greater Bay Area should, based on strengthening the integration of the higher education system within the Bay Area, closely track the economic transformation and industrial innovation of the area, promptly assess talent shortages across various industries, and dynamically adjust the graduate education structure in a demand-oriented manner.