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Due to the particularity of biomedical industry, it has become necessary for biomedical enterprises to seek innovative research and development (R&D) cooperation to maintain advanced technologies and products in multiple fields. Under such circumstance, the biomedical industry has gradually formed a certain cluster to promote the development of the industry. So far, the biomedical industry cluster has formed in China, mainly within the Yangtze River Delta, Pearl River Delta, and Beijing-Tianjin-Hebei three urban agglomerations. Within the industrial clusters, the frequency of innovation cooperation among enterprises, universities, research institutions, and other relevant organizations in the biomedical area is high, and the capacity for innovation cooperation is strong as well. This paper used the representative cross-section data of cooperative patents from the medical science and technology patent database of China National Knowledge Infrastructure (CNKI), researching the R&D cooperation within the three major urban agglomerations in China from 2008 to 2016 (Yangtze River Delta Urban Agglomeration, Pearl River Delta Urban Agglomeration, Beijing-Tianjin-Hebei Urban Agglomeration) on total 36 cities' spatial pattern characteristics of biomedical cooperation and the influencing factors. The spatial interaction model was used to study the spatial, economic, political, and R&D influencing factors of cross-city cooperation. The degree of aggregation showed that cross-city R&D cooperation mainly occurred in well-developed and central cities of urban agglomerations. Econometric results revealed that spatial, economic, political, and R&D bias factors did have a significant impact on the frequency of biomedical R&D cooperation across cities., Competing Interests: The authors declare no conflict of interest., (Copyright: © 2023 Sun et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)