Cystic renal cell carcinoma (cRCC) is uncommon and surgical indication remains controversial. We compared radical nephrectomy (RN) with partial nephrectomy (PN) in patients with cRCC using data from the Surveillance, Epidemiology and End Results (SEER) database and a retrospective cohort including 106 cRCC patients hospitalized in Ruijin and Renji Hospitals from 2013 to 2022. The baseline characteristics between RN and PN groups in both cohorts were adjusted by propensity score-matching (PSM). A total of 640 patients were included in the SEER cohort. Before PSM, PN group in the SEER cohort had a lower level of T stage (p< 0.001) and comprised more Caucasians (p< 0.001). After PSM, RN was associated with worse overall survival (p< 0.001) and cancer-specific survival (p= 0.006) in contrast to PN. In the Chinese cohort, 86 patients who underwent PN and 20 patients who underwent RN were finally included. The mean proportions of estimated glomerular filtration rate preserved after RN were worse than PN. Therefore, PN should be preferred in cRCC patients.