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The topological structure and multidimensional proximity evolution mechanism of Guangzhou biomedical industry innovation network are studied by using cooperative patents and cooperative papers from 1998 to 2018 with Ucinet and PLS-SEM. Research shows: ① The evolution of the Guangzhou Biomedical Industry Innovation Network can be divided into three stages, which are the primary budding stage of 1998–2005, the steady development stage of 2006–2012, and the rapid development stage of 2013–2018; ② the number of subjects in the innovation network is increasing, and the types of subjects are constantly increasing. The innovation network has gone from small to large, from closed to open, and from simple to complex. Patents and papers cooperation networks show different characteristics at various stages; ③ the relationship between geographical proximity, cognitive proximity, organizational proximity, and innovation network differs in stages. The interaction of proximity varies with the content of innovation cooperation. Based on this result, we have put forward policy recommendations for different innovative content.