Against the backdrop of rapid social economy and scientific and technological development, intelligent medical technology expanded based on the Internet plays a crucial role in the innovation and development of the modern medical industry. Intelligent medical technology has completely changed the fixed medical methods of the past, and it can solve the isolated defects between various unit systems, greatly improving the overall informatization level of hospitals. This article analyzed the clinical diagnosis, prevention, and treatment of neurodyspepsia syndrome (NDS) in intelligent medicine. Dyspepsia can cause palpitations, vomiting, abdominal distension, dizziness, and other symptoms so that it can cause discomfort and pain in the middle or around the epigastric region. Therefore, it is necessary to make a correct diagnosis of neurodyspepsia in order to reduce the discomfort of patients. Intelligent medical technology is of great significance in improving patients’ symptoms. This study sets up a control group and an experimental group for the experiment. The control group used conventional medication technology, while the experimental group used intelligent medical technology to analyze the patient samples taken. By comparing the factors that affect patients with NDS, it was found that the physical function score of the experimental group was 6.3% lower than that of the control group. Intelligent medical technology has high diagnostic efficiency and can achieve rapid diagnosis of NDS, meeting the clinical diagnosis and prevention requirements of NDS.