Background: Ductal carcinoma in situ with microinvasion (DCIS-MI) is a subtype of breast cancer with good prognosis, for which both breast conserving surgery plus radiotherapy (BCS+RT) and mastectomy are feasible surgical methods, but their effects on the prognosis of patients are still unclear. Methods: We used the Surveillance, Epidemiology and End Results (SEER) database to extracted DCIS-MI patients who underwent BCS+RT or mastectomy between 2000 and 2014. Participants were divided into BCS+RT group and mastectomy group. We compared the breast cancer-specific survival (BCSS) and overall survival (OS) of the two groups using Kaplan -Meier method and Cox proportional hazard regressions before and after propensity score matching (PSM) with the landmark. Results: We selected 5432 patients, among which 2834 patients (52.17%) were in the BCS+RT group and 2598 patients (47.83%) were in the mastectomy group. With a 101 months median follow-up time in the overall cohort, both univariate and multivariate analysis showed that BCS + RT group showed significantly higher OS and BCSS compared with patients in the mastectomy group (P<0.001). After PSM, the BCS+RT and mastectomy groups consisted of 1902 patients, respectively. multivariate analysis also showed that compared with mastectomy, the BCS+RT showed significantly higher OS and BCSS (HR = 0.676, 95% CI = 0.540-0.847, P<0.001; HR = 0.565,95% CI = 0.354-0.903, P= 0.017). In addition, the subgroup analysis showed that BCS + RT is at least equivalent to mastectomy with respect to OS and BCSS in any subgroup. Conclusion: For patients with DCIS-MI, the prognosis of BCS+RT was superior to mastectomy.