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Spontaneous abortion (SA) is a common adverse pregnancy outcome that severely impacts women's physical and mental health. Polycyclic aromatic hydrocarbons (PAHs) are one of the most prevalent classes of environmental endocrine disruptors with known reproductive and developmental toxicity. The accumulation of PAHs and their effect on the incidence of SA should be investigated. In this study, PAHs were measured in human chorionic villi of 15 SA cases and 14 controls. The concentration of PAHs was significantly elevated in patients with SA compared to the controls (98.07 ± 25.50 μg/g vs 125.0 ± 24.28 μg/g, P = 0.0071). Genome-wide methylation analysis revealed that metabolic and apoptotic signaling pathways were involved in SA. Compared to controls, villous samples from patients with SA exhibited reduced succinate dehydrogenase complex iron sulfur subunit (SDHB) DNA methylation, increased SDHB expression, and decreased succinate levels. The accumulation of PAHs in villi was inversely associated with SDHB methylation levels in patients. Furthermore, phenanthrene (Phe) exposure decreased the proliferation of human trophoblast cells and increased the expression of SDHB. Taken together, PAHs exposure up-regulated SDHB level, suppressed succinate accumulation, and increased the risk of SA.