Silica nanoparticles (SiNPs) are widely used in various commercial applications, which inevitably increase the risk of human exposure. It's reported that SiNPs have toxic effects on fertility, however, the specific mechanism of female reproductive toxicity induced by SiNPs remains confusing. In this study, female C57BL/6 mice at the age of 8 weeks were administrated orally with SiNPs at doses of 0, 3, and 10 mg/kg bw. every day in the presence/absence of NAC for eight weeks. The results showed that SiNPs could cause damage to ovaries and reduce the number of ovarian follicles, which led to disruption of sex hormone, altered estrous cyclicity and decreased female fertility. In addition, SiNPs induced oxidative stress in the ovary, as manifested by increased ROS and MDA levels, decreased SOD activity and inhibition of the Nrf2/HO-1 signaling pathway. Further study revealed that exposure to SiNPs resulted in mitochondrial dysfunction and promoted autophagy mediated by PI3K/AKT/mTOR and PINK1/Parkin signaling pathways. Meanwhile, apoptosis is also involved in SiNPs-induced cell death in a cooperative and synchronized manner, as evidenced by an increase in apoptosis-positive cells and activation of the ATM/p53-mediated apoptotic pathway. The supplementation of NAC restored most of the reproductive characteristics of the mice to its physiological range. These results demonstrated that SiNPs could cause ovarian damage via inducing oxidative stress and mitochondrial dysfunction, which led to autophagy and apoptosis, and ultimately resulting in abnormal folliculogenesis and female subfertility.