Innovation-driven strategy has become an important national policy during the 13th Five-Year Plan.In the context of global economic growth slowdown，it is important to prioritize technology leadership in order to take advantage of resource allocation.Thus，as the most dynamic “experimental field” in regional cross-border cooperation，Guangdong Free Trade Area has promoted a series of reforms and explorations in the institutional innovation of the technological cooperation system among Guangdong，Hong Kong and Macao.In order to develop technology，it is necessary to transform the existing management systems and motivate the enthusiasm of technological institutions，the market and the third sector.In addition，stimulating the integration of cross-border elements is also crucial.On this basis，this essay aims to analyze the problems faced by the technological cooperation system among Guangdong，Hong Kong and Macao，based on which it also gives nine relevant suggestions.