In the process of building an innovative country, the co-agglomeration of sci-tech service industry and high-tech manufacturing industry has become an important carrier to optimize the allocation of innovation resources in high-tech manufacturing industry and promote innovation and development. Based on the related data of China’s 28 provinces, districts and municipalities during 2009-2017 and by using network SBM-DEA model and panel Tobit model, this paper studies the impact of co-agglomeration of sci-tech service industry and high-tech manufacturing industry on innovation efficiency and regional differences in technological R&D stage and research result transformation stage. The analysis shows that the innovation efficiency of high-tech manufacturing industry is generally low in sample regions, and the efficiency of transformation stage is lower than that of technological R&D stage. The co-agglomeration level of sci-tech service industry and high-tech manufacturing industry needs to be improved, showing a gradient decreasing pattern in the eastern, central and western regions. Overall, whether in the technological R&D stage or in the transformation stage, the co-agglomeration has a significantly positive effect on innovation efficiency. From the perspective of regional heterogeneity, the co-agglomeration has a significantly promoting effect on the two-stage innovation efficiency in the eastern region, while it has a promoting effect on the central region only in the stage of transformation, and it has a promoting effect on the western region only in the stage of technology R&D. Therefore, the government should actively guide and boost the co-agglomeration of sci-tech service industry and high-tech manufacturing industry, sufficiently bring into fully play its promoting innovation efficiency, use technological transaction marketization to promote research results transformation, meanwhile, combine regional comparative advantages to cultivate competitive advantage so as to boost the regional differential development of industrial agglomeration.