Objective To compare the effectiveness of MR and CT in the diagnosis and diagnosis of ovarian endometriosis cyst, and to evaluate the diagnostic value of CT. Methods Two hundred cases of patients with cystic lesions of the ovary from January 2011 to October 2015 were diagnosed in the hospital as the research object, all of which were diagnosed by CT and MR. Results The endometrial cyst accounted for 38.5%, teratoma 26%, 17.5% serous cystadenoma, 11% simple cysts, 7% mucinous cystadenoma, endometrial cyst of bilateral disease proportion is higher than other types of cysts, endometriosis cyst under the age of ovarian cyst, endometriosis cyst diameter lower than mature teratoma, serous cystadenoma above, mucinous cystadenoma, simple cyst, the difference was statistically significant (P<0.05). MR diagnostic sensitivity 89.61%, specificity 91.06%, positive predictive value of 86.25% and negative predictive value of 93.33%, the coincidence rate was 90.50%, CT was 90.91%, 88.62%, diagnosis of 83.33%, 93.97%, 89.50%, the difference was not statistically significant (P>0.05), in the study of "satellite capsule" accounted for 51.95%, sac high density lesions in 11.69%, cystic wall thickening in 25.97%, cystic mass in 10 39%, adhesion accounted for 18.18%, false negative in 7 cases, of which 3 cases of adhesion, cystic mass in 3 cases, 1 cases of cystic wall thickening, the difference was not statistically significant (P>0.05). Conclusion CT differential diagnosis of ovarian endometriosis cyst is similar to MR, and the diagnostic utility of MR has no obvious advantage.