Background Metabolic syndrome (MetS) is an important factor related to the poor prognosis of breast cancer (BC). Molecular heterogeneity in the tumor may affect the consequence of BC. The main purpose of this study was to assess the prognostic link between MetS and the different BC molecular subtypes. Methods A total of 960 patients with BC were recruited from January 2010 to June 2014. The relationship between MetS and disease prognosis was assessed by using univariate and multivariate analyses. Results At recruitment, MetS was diagnosed in 199 patients (20.7%). The mean follow-up period was 68.5 months (range, 2–103 months). MetS remained significantly associated with 64% increased risk of recurrence (Hazard Ratio (HR)=1.64; 95% confidence interval (CI) 1.19–2.27, P<0.01) and twofold increased risk of mortality (HR=2.02, 95% CI 1.29–3.16, P<0.01) according to multivariate analysis. By reviewing BC molecular subtypes, the significant associations remained in the subsets of Luminal A (HR=3.1, 95% CI 1.28–4.57, P=0.01), Luminal B (Her2-negative) (HR=3.3, 95% CI 1.31–8.33, P=0.01), and Her-2-positive (non-Luminal) (HR=2.2, 95% CI 1.10–4.39, P=0.03). Conclusions MetS was significantly related to unfavorable prognosis in operable BC, especially in the subgroup of Luminal A. More studies are needed to definitively determine which factors influence the association of MetS with Luminal A subtype.