Abstract Study question To investigate the influence of ovarian endometriomas(OEM) surgery or not on the outcome of in vitro fertilization and embryo transfer. Summary answer Laparoscopic surgery can not significantly improve the outcome of IVF-ET in OEM patients, but may decrease the ovarian reserve. What is known already Despite the great advantages of ovarian endometriomas surgery treatment in endometriosis-linked infertility, the impact of laparoscopic cystectomy on outcomes of infertility management with ART is controversial. Numerous mechanisms have been proposed in an effort to delineate the multifaceted pathophysiology that induces impairment of reproductive dynamics in patients with OEM. Reactive oxygen species, dysregulation of the immune system and iron overload constitute the crucial mechanisms that detrimentally affect oocyte and embryo developmental potential. Study design, size, duration This study retrospectively included 882 cycles in our reproductive center from January 2018 to December 2020, and the patients were divided into operation group (n = 386) and OEM group (n = 496) according to whether they underwent laparoscopic cystectomy before IVF-ET. Participants/materials, setting, methods The baseline data of age, infertility duration, basic FSH, AFC, and BMI were used as matching factors, and Propensity score matching was carried out according to the sample ratio of 1:1, and 327 cycles in the operation group and 327 cycles in the OEM group were finally included. Follicular fluid was collected under ultrasound guidance during oocyte retrieval. A total of 74 follicular fluid samples meeting the study conditions were collected. Main results and the role of chance (1)The clinical pregnancy rate of fresh embryo transfer cycle in the OEM group was significantly higher than that in the operation group (77.4% Vs 52.9%), and the difference was statistically significant (P = 0.039). There was no significant difference in pregnancy outcome in frozen embryo transfer cycle (P > 0.05). (2) The results of Multi-factor logistic regression model showed the clinical pregnancy rate of patients in the OEM group was 3.048 times than that of patients in the operation group in fresh cycle, and the difference was significant (OR 3.029 95%CI 1.017-9.018, P = 0.047), while early abortion and live birth pregnancy outcomes were not significantly affected in both groups. For the frozen embryo transfer cycle, there were no significant effects on clinical pregnancy, early abortion and live birth pregnancy outcomes in both groups. (3) There was no significant difference in follicular fluid iron concentration between OEM group and control group(11.53±3.38 Vs 12.18±4.37μg/dl, P = 0.112). The concentration of ferritin in follicle fluid in OEM group (57.38±139.90) was significantly higher than that in control group (24.88±13.76 μg/ml), the difference was statistically significant (P = 0.032). Limitations, reasons for caution The present study being of a retrospective and monocentric study, may not come to a very convincing conclusion, and some unknown biases might still exist due to possible underestimation of some confounders. Wider implications of the findings Collectively, our results indicate that laparoscopic ovarian cystectomy couldn’t significantly improve the IVF-ET outcomes in patients with OEM, but rather increased the risk of reduced ovarian reserve function. Ovarian reserve function was the main factor affecting the IVF-ET outcomes for infertile patients with OEM. Trial registration number /