Current knowledge of the association between peripheral natural killer (NK) cell proportion and ovarian function in reproductive-age women is limited. We explored the association between NK cell proportion and ovarian function in women who underwent in-vitro fertilization (IVF) treatment. This was a retrospective cohort study using the data of 20–44-year-old women with recurrent implantation failure (RIF) who were tested for NK cell proportion and anti-Müllerian hormone (AMH). Indicators of ovarian function included AMH, observed-to-(age-appropriate) reference AMH ratio, high FSH, peak E2 and total number of oocytes during the first IVF cycle following the test. We used different model specification controlling for women’s age, and body mass index. Among a total of 936 women, majority showed lower AMH compared to age-appropriate level. Average NK cell proportion was 13.5 ± 5.7%. Number of oocytes showed positive association with NK cell (ß = 0.040, p = .025). In the subgroup with NK ≥ 18%, NK cell proportion was negatively associated with AMH (−0.106, p = .012), AMH ratio (−0.049, p = .014) and number of oocytes (−0.021, p < .001) while the associations with others remain close to null. High NK cell proportion may be harmful to ovarian reserve or function.