Medical innovation has consistently been an essential subject and a source of support for public health research. Furthermore, improving the level of medical research and development is of great concern in this field. This paper highlights the role of big data in public medical innovation. Based on a sample of China’s listed firms in the medical industry from 2013 to 2018, this paper explores the exogenous shock effect of China’s big data medical policy. Results show that the construction of the medical big data platform effectively promotes innovation investment and the innovation patent of medical firms. In addition, the heterogeneity of this promoting effect is reflected in firm size through the overcoming of different innovation bottlenecks. The research conclusions support the positive significance of the macro-led implementation of the medical big data platform, and suggest that the positive economic externalities generated by this policy are critical to public health.