Hexachlorobenzene (HCB), a widespread environmental pollutant, contributes to endocrine disruption resulting in hypothyroidism. We investigated the effect of chronic exposure of HCB to explore the functional interconnection between hypothyroidism and infertility. All observations were made through the F1 and F2 generations. Thyroidectomy was also performed to evaluate the contribution of the thyroid gland in affecting ovarian dysfunction and reproductive aberrations. We confirmed that the preconception exposure of HCB leads to hypothyroidism which was reflected by an increase in the body weight, alteration in the thyroid hormones, and alteration of the lipid profile. Hypothyroid female rats exhibited a poor reproductive profile with altered steroidogenic pathways, altered estrus cyclicity, reduced litter size, and stunted growth. The external supplementation of thyroxine in thyroidectomized animals rescues the reproductive aberrations confirming the protective role of the thyroid gland in reproductive biology. All results highlight the jeopardizing functional connection of the thyroid and ovary due to HCB, leading to serious consequences on upcoming generations.