Background Ovarian reserve, vital for reproductive function, can be adversely affected by thyroid diseases. Despite alternations of thyroid hormones with ageing, data on interactions between the overtime trend of thyroid functions and ovarian reserve status has rarely been reported. We aimed to examine the overtime trend of thyroid hormones, thyroid peroxidase antibody (TPO Ab) and their associations with ovarian reserve status, identified by levels of age specific anti-mullerian hormone (AMH) in reproductive aged women, who participated in 12-year cohort of Tehran Thyroid Study (TTS). Methods Reproductive age women( n = 775) without any thyroid disease or ovarian dysfunction were selected from the Tehran Thyroid Study cohort. Participants were divided into four age specific AMH quartiles (Q1-Q4), Q1, the lowest and Q4, the highest. AMH was measured at the initiation of study and thyroid stimulating hormone (TSH), free T4 (FT4), and TPO Ab were measured at baseline and at three follow up visits. Results At baseline, there was no statistically significant difference in thyroid hormones between women of the four quartiles, although TPO Ab levels were higher in women of Q1. During the follow ups, FT4 was decreased in all quartiles ( p < 0.05), whereas TPO Ab increased in Q1 ( p = 0.02). Odds ratio of overall TPO Ab positivity in women of Q1 was 2.08 fold higher than those in Q4. (OR: 2.08, 95%CI: 1.16, 3.72; p = 0.01). Conclusion Women with the lowest ovarian reserves had higher levels of TPO Ab, with a positive trend of this antibody overtime in comparison to other quartiles, indicating that this group may be at a higher risk of hypothyroidism over time.