The development of medical detection, storage, and other technologies makes China’s medical and health field accumulate massive data. Big data analysis technology can mine and analyze these data and establish medical information systems to enhance hospital treatment and service levels. Therefore, this work studies the construction and application of medical economic information systems. Specifically, neural networks, as a means to handle a large number of medical economic data, and has received great attention. This work uses BP neural network to extract the medical economic information feature, which is a big data technology and can extract deep features of data, after that, we compare and analyze the characteristic of different medical data. Finally, we establish the medical economic information system for the follow-up medical diagnostic services.