The logistics industry and the manufacturing industry are mutually productive factors and service objects, which determines that the two must develop cooperatively. In the increasingly fierce market competition, open collaborative innovation is more conducive to improving the level of linkage between the logistics industry and the manufacturing industry, and promoting industrial development. Based on the patent data of 284 prefecture-level cities in China from 2006 to 2020, this paper uses Gis spatial analysis, spatial Dubin model and other methods to analyze the collaborative innovation between the logistics industry and manufacturing industry. The results lead to several conclusions. (i) The overall collaborative innovation level is not high, and in terms of the evolution cycle, collaborative innovation has experienced three stages: embryo, rapid development and stable development. (ii) The spatial agglomeration characteristics of the collaborative innovation between the two industries are more and more obvious, and the Yangtze River Delta urban agglomeration and the middle reaches of the Yangtze River urban agglomeration play an important role in the collaborative innovation between the two industries. (iii) The hot spots of collaborative innovation between the two industries are concentrated in the eastern and northern coastal areas, while the cold spots are concentrated in the south of the northwest and southwest areas in the late stage of the study. (iiii) The positive influencing factors of local collaborative innovation between the two industries include economic development, scientific and technological level, government behavior, and employment, while the negative influencing factors include information technology level, and logistics infrastructure. Economic development has a negative spatial spillover effect on surrounding areas, while the spatial spillover effect of scientific and technological level is significantly positive. This article aims to explore the current situation and influencing factors of collaborative innovation between the two industries, with a view to proposing countermeasures and suggestions for improving the level of collaborative innovation between the two industries, and also providing new ideas for research on cross industry collaborative innovation.