Based on an overview of the concepts related to the regional innovation system，a new definition is made for the regional innovation system. The core characteristics of the regional innovation system is identified as：an “active allocation mechanism” that takes innovation as the goal and promotes the combination of resources and elements inside and outside the region as “innovative destruction”；the “active allocation mechanism” in the regional innovation system that mainly determined by the “predictability” of the socio-economic operating environment at the core of the rule of law and the “efficiency” of the mechanism of allocating resources and factors. Based on the analysis of the positioning and status of the Guangdong-Hong Kong-Macao Greater Bay Area regional innovation system，this article proposes several countermeasures on the “Active Allocation mechanism” that government functions and construction needs to be changed in accordance with the requirements of market economy development，that a business environment conducive to innovation and development must be made，and that mechanism construction by activating the “Guangzhou-Shenzhen-Hong Kong-Macao Innovation Corridor” must be promoted.