Polycystic ovary syndrome (PCOS) is the most common endocrine disease afflicting women of childbearing age. It is characterized by irregular menstruation, clinical or biochemical hyperandrogenemia, and polycystic ovary morphology. As a complex endocrine-metabolic syndrome (MS), PCOS shares several endocrine-metabolic features with the MS, with insulin resistance at the core of their pathogenic mechanisms. PCOS and MS are interrelated and thus have similarities in treatment. Currently, the common treatment modalities for both are lifestyle intervention, medication, and surgery. More studies have shown that lifestyle intervention and regulation of intestinal flora are more effective and sustainable. However, progress towards treatment and cure is hampered by unclear etiology and mechanisms. This review aimed to summarize the relationship between PCOS and MS, the pathogenesis of metabolic disorders, and the current nutritional therapeutic strategies, especially lifestyle modifications and modulation of intestinal flora. Lifestyle interventions combined with the regulation of gut flora can be a new perspective for treatment. This perspective has a positive significance in the early diagnosis, adoption of personalized treatment plans, and prevention of complications in PCOS and MS. The need to prevent the occurrence of MS in patients with PCOS should be emphasized.