Objective This paper is to investigate clinical value of CT and MRI in diagnosis of prostate cancer, and to provide theoretical basis for improving clinical diagnostic rate. Methods The method of comparative study was applied to conduct investigation on 70 patients with prostate cancer from December, 2013 to December, 2014, all patients underwet CT examination (control group) and MRI (research group), and advantages and disadvantages of two types of inspection method were compared on the basis of histopathologic diagnosis. Results The comparisons in consistent diagnosis rate, misdiagnosis rate and the rate of missed diagnosis of patients in two groups in the diagnosis of prostate cancer of patients at Stage A and Stage B on the basis of pathological biopsy satisfied χ2 =40.17, 17.69 and 12.99 (P<0.05) respectively, the differences were significantly statistical, and there was no difference between the two groups of patients in the diagnosis of patients with prostate cancer at stage C and D. Conclusions MRI delivers high accuracy in the diagnosis of prostate cancer, and it can be used and promoted in auxiliary examination of clinical evaluation on patients in stages way, CT casts diagnostic rate of patients with prostate cancer at Stage A and Stage B, and high accuracy is only founded in the diagnosis at Stage C and Stage D, therefore it is not recommended to be used in the diagnosis of early prostate cancer.