Objective To investigate the differences of renal function indexes between patients with renal cysts and cystic small renal cell carcinomas and to explore the application value of CT examination in the differential diagnosis of the two diseases. Methods Two hundred and four cases of patients with simple renal cysts (study group A) and 15 cases of patients with cystic small renal cell carcinoma (study groupB) were selected as the study subjects, and all of them were confirmed by operation and pathology. 60 healthy volunteers who received physical examination in the hospital during the same period were chosen as the control group. All the three groups received renal function examination. Patients in the two study groups received CT scan and enhanced scan at the same time. The renal function indexes were compared among the three groups; Based on the results of pathological diagnosis, the accuracy of CT examination in the differential diagnosis of cystic small renal cell carcinoma and simple renal cysts was evaluated. Results The detection results of SCr and BUN in the three groups of subjects show the control group < study group A < study group B while eGFR showed control group > study group A > study group B (P<0.05). The accuracy of CT in differential diagnosis of cystic small renal cell carcinoma and simple renal cysts was 85.8% (188/219), in which 178 cases (87.3%, 178/204) with simple renal cysts and 10 cases (66.7%,10/15) with cystic small renal cell carcinoma were diagnosed correctly. Conclusion Both of patients with simple renal cysts and cystic small cystic renal cell carcinoma have abnormal renal function indexes, which is worthy of attention; Although the spiral CT findings of the two diseases are specific, there are risks of missed diagnosis and misdiagnosis in the diagnosis of lesions with smaller occupied volume. It is suggested that CT can be used as an assisted differential diagnosis method in clinical diagnosis and treatment.