Background: The impact of polycystic ovary syndrome (PCOS) on endometrial receptivity and embryo quality is a subject of debate. Different PCOS patient types may exhibit different effects on these factors. This study aimed to identify causes for low live birth rate by comparing endometrial receptivity and embryo quality among different PCOS types. Methods: Overall, a total of 767 PCOS patients with first in vitro fertilization (IVF)/intracytoplasmic sperm injection (ICSI) treatment classified into phenotype A (n = 167 patients) and phenotype D (n = 600 patients) were eligible for analysis. Patients with single polycystic ovary (n = 406 patients) served as a control group to exclude the advantages of clinical outcome from higher number of oocytes retrieved in women with PCOS. Results: In phenotype A and D, Anti-Müllerian hormone (AMH), antral follicle count (AFC) and basic estradiol were significantly higher compared to single polycystic ovary. However, estradiol, progestin and endometrial thickness on the human chorionic gonadotropin (hCG) day were significantly decreased. In fresh cycles, phenotype A had a significant statistical decrease in the live birth rate compared with single polycystic ovary (35/78 [44.87%] vs. 135/233 [57.94%], p 0.05), although there was no significant difference in the number of embryo transplants and clinical pregnancy rate among the three groups. It might be associated with the significant reduction of total gonadotropin (Gn) dose, Gn duration, and follicular output rate (FORT) in all the typed PCOS groups. In the first frozen embryo transfer (ET) cycles, no significant difference was observed for estrogen, progestin, or endometrial thickness on the day of ovulation and live birth rate. Women with live birth had a higher estradiol on the hCG day in the phenotype A (3763 [3121, 4752] vs. 2954 [2112, 4036] ng/mL) while a lower estradiol in the single polycystic ovary (3312 [2341, 4465] vs. 3417 [2350, 4638] ng/mL). In multivariate logistic regression analysis, estradiol on the hCG day was a significant independent factor predicting live birth for women with phenotype A (odds ratio (OR) >1.000, 95% confidence interval (95% CI): 1.000–1.001), p = 0.034) and single polycystic ovary (OR 1.000, 95% CI: 0.999–1.000, p = 0.013) in fresh ET. Conclusions: The various subtypes of PCOS have no significant adverse effect on embryonic outcome. It was not directly caused by PCOS; however, low levels of estradiol may be the reason for the low live birth rate owing to significant reduction of total Gn dose, Gn duration and FORT as a result to low incidence of ovarian hyperstimulation syndrome (OHSS) in phenotype A.