Background/Objectives: Polycystic ovary syndrome (PCOS) is a heterogeneous endocrine disorder associated with systemic inflammation, metabolic dysfunction, and altered intestinal permeability. Emerging evidence suggests interactions between oral health and systemic inflammatory pathways; however, phenotype-specific associations between oral hygiene status and systemic biomarkers in PCOS remain unclear. This study aimed to evaluate the relationship between oral hygiene indices and inflammatory, metabolic, and intestinal permeability biomarkers in women with classical and non-classical PCOS. Methods: This cross-sectional study included 83 women, consisting of 39 patients with classical PCOS and 44 patients with non-classical PCOS. Oral hygiene status was assessed using the Oral Hygiene Index–Simplified (OHI-S), including debris and calculus scores. Serum interleukin-1 beta (IL-1β), anti-Müllerian hormone (AMH), zonulin, and Homeostatic Model Assessment of Insulin Resistance (HOMA-IR) were measured using enzyme-linked immunosorbent assay. Statistical analyses were performed to compare group characteristics and evaluate phenotype-specific correlations between oral hygiene indices and systemic biomarkers. Results: No significant differences were observed in debris score, calculus score, total OHI-S score, IL-1β, AMH, zonulin, or HOMA-IR among classical PCOS, non-classical PCOS, and control groups. In classical PCOS, the calculus score was negatively correlated with zonulin levels (ρ = −0.37; p = 0.022). In non-classical PCOS, debris score and total OHI-S score were positively correlated with zonulin levels (ρ = 0.46, p = 0.002 and ρ = 0.37, p = 0.013, respectively). No significant correlations were identified between oral hygiene indices and IL-1β, AMH, or HOMA-IR. Conclusions: Oral hygiene status and systemic biomarker levels did not differ significantly between women with PCOS and healthy controls. However, phenotype-specific associations between oral hygiene indices and zonulin suggest a potential role of the oral–intestinal axis in PCOS pathophysiology, particularly in non-classical PCOS.