This research based on the theory of integrated development of service sector and industrial sector，literature review and mechanism analysis are carried out. And，model is used to evaluate the integration development of service sector and industrial sector，and its effect on technological innovation are studied. Furthermore，we put forward some measures to drive the innovative development of Guangdong-Hong Kong-Macao Greater Bay Area with deep industrial integration，which includes：expanding the effective service supply to meet the upgrading demand of Guangdong-Hong Kong-Macao Greater Bay Area，integrate into the new generation of information technology to promote the innovation of service sector，strengthen the cross-border integration of service sector and promote the high-end of industrial value chain，enhance the opening-up level of service sector and accelerate the level of internationalization，cultivate quality standard brands and improve the quality and efficiency of service sector，optimize the spatial layout of service sector and promote the coordinated development of different industries，deepen the comprehensive reform and achieve innovation vitality of the innovation policy of service sector.