The industry-academy cooperation facilitated the growth both in production and in economy.In the background of regional economic cooperation，the collaboration for innovation and development among private enterprises，educational institutions and governments had become the objective requirement for the further development and transformation industries in Guangdong and Hong Kong，especially the economic development in the Great Bay District，a product of Guangdong and Hong Kong cooperation，calling more many-sided cross-field cooperation to achieve the preset goal.Based on empirical research，the paper found the causes for disparity in industry-academy cooperation hindering the further development of the cooperation，and the research result was significant in following the benefit structure and characteristics of industry-academy cooperation in cities of Guangdong and Hong Kong，and provided a practical reference for the further development and construction of industry-academy cooperation.