Objective This paper is to investigate clinical diagnosis value of CT and MRI on cystic lesions of pancreas, to provide the reference for clinical diagnosis in the future, and to improve the diagnosis level on cystic lesions of pancreas. Methods Thirty eight patients with cystic lesions of pancreas admitted by the Hospital were selected as research subjects, patients underwent CT and MRI diagnosis respectively, pathological examination findings of CT and MRI on patients were subject to comparative analysis, and clinical diagnosis value of CT and MRI on cystic lesions of pancreas was explored. Results The difference between CT and MRI examination findings and pathological findings was of no statistical difference when compared, and the differences between were CT and MRI examination findings not statistically important. The duration of MRI examination was less than that of CT examination (p<0.05), and the difference was statistically significant. Conclusions CT and MRI deliver significant clinical value in the diagnosis of CSTP, the images show certain characteristics, the duration of MRI examination is longer than that of CT diagnosis, but it is provided multi-dimensional imaging, it is capable of providing more information on the cystic component, and it is especially particularly sensitive to haemorrhage. The diagnostic mode suitable for patients should be selected according to specific conditions of patients in clinical practices to provide important diagnosis basis for follow-up treatments of patients.