Objective To provide valuable insights for the government and research institutions to formulate international cooperation strategies and policies by analyzing the international collaboration preferences of different cities in the field of biomedical engineering in China. Methods Biomedical engineering journal articles published in recent 3 years were retrieved from the Web of Science database. Collaborative networks were constructed based on cities and institutions in the authorship of papers. Subsequently, the betweenness centrality and clustering coefficient of each city and institution in the collaborative network were calculated to assess collaboration preferences. Nodes with high betweenness centrality and low clustering coefficients were classified as the first type (preferring international collaboration), those with moderate betweenness centrality and clustering coefficients were classified as the second type (no clear preference), and those with low betweenness centrality and high clustering coefficients were classified as the third type (preferring domestic collaboration). Results Analysis at the city level reveals that Shanghai and Beijing consistently belong to the first category. Shenzhen, Guangzhou, Hong Kong, Hangzhou, Nanjing remain in the second category, with Chengdu transitioning from the third category to the second category in 2023. Tianjin, Chongqing, Xi'an, Taipei, Hefei, Harbin, Wuhan, Suzhou, Shenyang, and Jinan consistently fall into the third category. At the institution level, Shanghai Jiao Tong University consistently belongs to the first category, while Zhejiang University and Fudan University remain in the second category. Sun Yat-sen University, Sichuan University, Chinese Academy of Sciences, and Peking University enter the second category in certain years. Tsinghua University, Southern Medical University, Beihang University, University of Chinese Academy of Sciences, Capital Medical University, Tianjin University, South China University of Technology, Southeast University, University of Science and Technology of China, and Soochow University consistently fall into the third category. Conclusions Research institutions in Beijing and Shanghai are the most active in international collaboration in the field of biomedical engineering, with Shanghai Jiao Tong University, Chinese Academy of Sciences, and Peking University being prominent representatives. Hangzhou and Nanjing in the Yangtze River Delta and Shenzhen, Guangzhou, and Hong Kong in the Greater Bay Area also exhibit strong enthusiasm for international collaboration, represented by institutions such as Zhejiang University, Fudan University, and Sun Yat-sen University. Chengdu, in the western region, has significantly increased its international collaboration efforts, with Sichuan University being the most prominent contributor. Research institutions in other cities tend to collaborate more with domestic institutions.