Although some observational studies suggest an inverse association between omega-3 fatty acids and fracture risk, recent randomized controlled trials have yielded conflicting results. Few studies have focused on high-risk populations, such as postmenopausal women with metabolic syndrome (MetS), in whom both metabolic and skeletal vulnerabilities coexist. We conducted a propensity score-matched cohort study using a Korean National Health Insurance Service (NHIS) customized database to compare fracture outcomes between postmenopausal women with MetS receiving statins alone versus statins combined with omega-3 fatty acids. A total of 14,312 women who used statins alone for ≥180 days (Statin only group) were matched (1:1–2 ratio) with women who received combined treatment (Statin with omega-3 group). Multivariable Cox proportional hazards models were used to estimate fracture risk. The Statin with omega-3 group showed a significantly lower risk of major osteoporotic fractures (HR 0.84, 95% CI 0.73–0.96; p<0.01), particularly non-vertebral fractures (HR 0.79, 95% CI 0.64–0.98; p=0.032), while vertebral fracture risk was not significantly different (HR 0.86, 95% CI 0.71–1.03). A dose-response relationship was observed: compared to the Statin only group, the HRs were 0.81 (≤1g/day), 0.75 (1.1–1.9g/day), and 0.63 (≥2g/day). Each 1g/day increase in omega-3 dosage was associated with a 14% reduction in fracture risk (HR 0.86; 95% CI 0.82–0.91; p<0.001). These findings suggest that the addition of omega-3 fatty acids to statin therapy may offer skeletal benefits beyond lipid-lowering effects, particularly in postmenopausal women with MetS. This supports the concept of metabolic health–bone health crosstalk, wherein interventions targeting metabolic dysregulation may concurrently influence fracture risk. Omega-3 supplementation may thus play a supportive role in maintaining skeletal integrity in this population, meriting further investigation into its pleiotropic effects and therapeutic implications across metabolic and musculoskeletal domains.