Objective To explore the clinical diagnostic value of MRI combined with carbohydrate antigen 125 (CA125) and carbohydrate antigen 199 (CA199) in the diagnosis of stage I epithelial ovarian cancer. Methods A total of 49 cases of patients with stage I epithelial ovarian cancer confirmed by pathological section were selected as observation group, and 42 cases were benign gynecological diseases and were selected as benign group, and 53 healthy examiners were included into control group. MRI data and serum contents of CA125 and CA199 were compared and analyzed in the three groups. Results There was a statistically significant difference in the serum CA125 level among control group, benign group and observation group (F=33.630, P<0.05). There was a statistically significant difference in the serum level of CA199 in the three groups (F=28.017, P <0.05). Compared with the positive detection rate of individual indicators, the positive detection rate of combined CA125 and CA199 was significantly increased (P<0.05), and the positive detection rate of combined MRI and serum factors CA125 and CA199 was significantly increased (P<0.05). Compared with the sensitivity of individual indicators, the sensitivities of combined CA125 and CA199, and combined MRI and serum factors CA125 and CA199 were increased. Conclusion The positive rate of MRI combined with serum factors CA125 and CA199 is increased in the detection of stage I epithelial ovarian cancer, which is beneficial to improve the clinical diagnosis rate of patients with stage I epithelial ovarian cancer.