Background: Many studies have demonstrated the positive clinical value of progestin-primed ovarian stimulation (PPOS) in patients with polycystic ovary syndrome (PCOS) who underwent assisted reproductive technology. However, the underlying factors contributing to this phenomenon remain unclear. We conducted a retrospective observational study to compare the clinical outcomes of women with PCOS who underwent PPOS or the short protocol to identify possible factors that influence the outcome. Methods: This study included 304 patients who underwent PPOS and 152 patients who underwent short protocol from April 2014 to July 2019 after propensity-score matching. Human menopausal gonadotropin (hMG) dose, hormone profile, embryo development, and clinical outcomes of frozen-thawed embryo transfer (FET) cycles were compared. The primary outcome measure was the implantation rate. Logistic regression was performed to identify contributing factors, and receiver operating characteristic curve analysis was used to calculate the cutoff of luteinizing hormone (LH) difference ratio in clinical outcomes. Results: Compared with the short protocol, PPOS resulted in a higher implantation rate (43.4% vs. 31.9%, P < 0.05), clinical pregnancy rate (61.8% vs. 47.4%, P < 0.05), and live birth rate (48.4% vs. 36.8%, P < 0.05). Similar fertilization, cleavage, and valid embryo rate per oocyte retrieved between groups were observed. The LH difference ratio was positively associated with implantation rate [P = 0.027, odds ratio (OR) = 1.861, 95% CI: 1.074–3.226]. The relationship between the LH difference ratio with clinical outcomes was confirmed by receiver operating characteristic curve analysis and comparisons among patients grouped by the LH difference ratio. Conclusion: The implantation rate was associated with the LH difference ratio during ovary stimulation in patients with PCOS. Our results provide the explanation why PPOS shows the positive clinical outcomes for patients with PCOS.