Objective: To describe the gross and histological characters of MRKHS patients’ ovaries and assess their ovarian reserve directly for future pregnancy. Design: A prospective case-control study. Setting and population: A prospective case-control study involving 67 MRKH syndrome patients and 17 ovarian biopsies (with age-matched controls), from January 2017 to February 2020. Methods: We observed the gross appearance of 67 Chinese MRKHS patients during laparoscopically assisted neovagina creation surgery. Seventeen ovarian biopsies were obtained and compared with age-matched controls for the histological characters. Twelve biopsy specimens underwent a complete serial section and calculation of the primordial follicular density. Main Outcome Measures: Follicle density, morphology in ovarian cortex biopsies. Results: 5/67 MRKHS patients’ ovaries had abnormal gross appearance, including streak gonads and bilateral porcelain white ovaries. We observed corpus luteum or corpus albicans on 5/8 patients under 20 years old, but none of the controls. None of the biopsies from MRKHS type Ⅱ patients showed corpus luteum or corpus albicans. Two type Ⅰ patients presented with compromised ovarian reserve, and significant increase of atretic follicles and corpus albicans. A significant inverse correlation was observed between primordial follicular density and age in 12 patients aged 16 to 25 years old. Conclusion: The ovaries of MRKHS patients have higher rates of abnormalities regarding gross appearance and histological characters. Tweetable abstract: It is suggested that early preparation for fertility reserve and incorporated as a part of the treatment when reconstructing the neovagina in MRKH syndrome patients due to premature declination of the ovarian reserve.