Malignant phyllodes tumor of the breast (MPTB) is a rare type of breast cancer. The prognosis between breast-conserving surgery (BCS) and mastectomy remains unclear in MPTB. Therefore, long-term survival was investigated between BCS and mastectomy in MPTB via the Surveillance, Epidemiology, and End Results (SEER) database. MPTB patients with T1-2/N0 stage between 2000 and 2015 from SEER database were retrospectively reviewed. Prognosis between different surgical approaches was assessed by Kaplan-Meier curves and Cox proportional hazards analysis. A total of 795 patients were enrolled with a median follow-up of 126 months. BCS was associated with significantly increased 10-year overall survival (OS) (89.2% vs. 81.1%, p = 0.002) and breast cancer-specific survival (BCSS) (95.2% vs. 90%, p = 0.004) compared with mastectomy. Multivariate analysis showed better OS (HR = 0.587, 95% CI 0.406-0.850, p = 0.005) and BCSS (HR = 0.463, 95%CI 0.267-0.804, p = 0.006) in the BCS group than the mastectomy group. After 1:1 propensity score matching (PSM), improved 10-year OS (89.2% vs.81%, p = 0.023) and BCSS (95.8% vs. 90.1%, p = 0.033) were observed in BCS compared with mastectomy. This study found the survival benefit of BCS over mastectomy in patients with early-stage MPTB. BCS should be recommended as a priority in MPTB patients when both surgical approaches are feasible.