Although the Internet of Things has been widely applied, the problems of cloud computing in the application of digital smart medical Big Data collection, processing, analysis, and storage remain, especially the low efficiency of medical diagnosis. And with the wide application of the Internet of Things and Big Data in the medical field, medical Big Data is increasing in geometric magnitude resulting in cloud service overload, insufficient storage, communication delay, and network congestion. In order to solve these medical and network problems, a medical big-data-oriented fog computing architecture and BP algorithm application are proposed, and its structural advantages and characteristics are studied. This architecture enables the medical Big Data generated by medical edge devices and the existing data in the cloud service center to calculate, compare and analyze the fog node through the Internet of Things. The diagnosis results are designed to reduce the business processing delay and improve the diagnosis effect. Considering the weak computing of each edge device, the artificial intelligence BP neural network algorithm is used in the core computing model of the medical diagnosis system to improve the system computing power, enhance the medical intelligence-aided decision-making, and improve the clinical diagnosis and treatment efficiency. In the application process, combined with the characteristics of medical Big Data technology, through fog architecture design and Big Data technology integration, we could research the processing and analysis of heterogeneous data of the medical diagnosis system in the context of the Internet of Things. The results are promising: The medical platform network is smooth, the data storage space is sufficient, the data processing and analysis speed is fast, the diagnosis effect is remarkable, and it is a good assistant to doctors’ treatment effect. It not only effectively solves the problem of low clinical diagnosis, treatment efficiency and quality, but also reduces the waiting time of patients, effectively solves the contradiction between doctors and patients, and improves the medical service quality and management level.