Nanotechnology is employed in a number of different sectors, including agriculture, food production, and medicines. However, excessive exposure has been linked to a range of severe health effects. To estimate the correct dosage and extrapolate animal toxicity data to humans, detailed information of NPs toxicity is required. Unfortunately, inadequate consideration has been paid to the potential that nanoparticles (NPs) might have a detrimental effect on female reproductive health. In the current study, healthy female rats were given daily doses of multiwalled carbon nanotubes (MWCNT; 5mg/kg BW), zinc Oxide (ZnO; 5mg/kg BW), and mesoporous silica nanoparticles (MSN; 15mg/kg BW). The primary abnormalities were found to be a reduction in body weight, ovary size, follicle count, and follicular cyst development. The ICP-MS results demonstrated the presence of ZnO and MSN in liver, kidney, spleen and ovary. When compared to control, the biodistribution of ZnO and MSN in the ovary was 1.14 and 1.41 times that of Zn and Si, respectively. Thus, the ovarian function is affected by the translocation of ZnO and MSN from the systemic circulation to the ovary. According to the proteomics findings, the differentially expressed proteins include several critical proteins involved in oxidative stress, reproduction, metabolic activities, cytoskeletal dynamics, cell cycle, cell death, and inflammation. NPs affect angiogenesis and extracellular matrix stabilization which is required for follicle development, and they are both mediated by the proteins Pdlim1, Shroom3, Tagln, and TGF-β. Animals treated with MWCNT and ZnO NPs revealed an altered expression of Sox4, Fbxo45, Unc13c, Brsk1, Pde3a, and EphB4 proteins which may contribute to the problems associated with follicle development. TNF-α and IL-1β levels are the most significantly altered by ZnO NPs exposure and are associated with decreased fertility and ovarian damage. We conclude that ovarian tissue is an excellent model for studying environmental xenobiotics.