The promise that big data will revolutionize scientific discovery and technology innovation is now being widely recognized. With the explosive growth of biomedical data, life science is being transformed into a digital science in which novel insights are gained from in-depth data analysis and modeling. Extensive and innovative utilization of biomedical big data is a key to the success of precision medicine. Therefore, constructing a centralized national-level biomedical big data infrastructure becomes crucial and urgent for China. Such infrastructure should achieve superb capacity of safe data storage, standardized data processing and quality control, systematic data integration across multiple types, and in-depth data mining and effective data sharing. Full data chain service including information retrieval, knowledge discovery and technology support can be provided to data centers, research institutes and healthcare industries. Relying on Shanghai Institutes for Biological Sciences, agreements have been signed that a main node of the infrastructure will be located in Shanghai, and a backup node will be set up in Guizhou Province. After a construction period of five years, the infrastructure should greatly enhance China’s core competence in collection, interpretation and application of biomedical big data.