Scientific and technological innovation is the key to improve the national core competitiveness，and regional innovation system is the pillar and backing of Country’s comprehensive strength and international competitivene-ss. Under the background of accelerating the formation of a new development pattern with the domestic big cycle as the main body and the domestic and international double cycles promoting each other，the Guangdong-Hong Kong-Macao Greater Bay Area is the specific carrier of regional innovation network，it is of great significance to promote the construction of regional innovation system in the Guangdong-Hong Kong-Macao Greater Bay Area. During the “14^th Five-Year Plan” period，the construction of national and regional innovation system will be continuously promoted，and at the same time，China’s regional innovation system will be built into a high level，open and regional collaborative innovation system. This report proposes that the basic ideas for the construction of the Guangdong-Hong Kong-Macao Greater Bay Area regional innovation system during the “14^thFive-Year Plan” period are：multi-level large bay area innovation infrastructure layout，cultivating regional innovation cluster，accelerate blend in and active global innovation network layout，improve the innovative elements configuration mechanism，finally strengthen the top-level design and planning guide，set up a high-level task force agencies to coordinate.