It is of great practical significance to promote the in-depth implementation of innovation-driven development strategy and promote the high-quality development of manufacturing industry in Shandong Province by constructing the scientific and technological innovation system of manufacturing industry and deepening the collaborative innovation of industry, university and research. The entropy method was used to evaluate the efficiency of the scientific and technological innovation system of manufacturing industry in Shandong Province. By comparing with Beijing, Shanghai, Guangdong, Jiangsu and Zhejiang, the current situation and challenges of the scientific and technological innovation system of manufacturing industry in Shandong Province were analyzed from three aspects, such as scientific research, technological innovation and industrial innovation. In order to promote the coordinated development of scientific and technological innovation of manufacturing industry in Shandong Province and build a new pattern of high-quality development, a deep collaborative development strategy is put forward and its feasibility is analyzed.