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Background and Objectives: To evaluate the impact of gonadotropin-releasing hormone agonist (GnRHa) triggering compared to human chorionic gonadotropin (hCG) triggering on frozen-thawed and fresh embryo transfer outcomes in patients with polycystic ovary syndrome (PCOS) undergoing in vitro fertilization (IVF). Materials and Methods: This retrospective cohort study analyzed 267 IVF cycles of 261 PCOS patients treated with GnRH antagonist protocols. Patients were divided into three groups: GnRHa-triggered frozen-thawed embryo transfer (ET) (n = 126), hCG-triggered frozen-thawed ET (n = 68), and hCG-triggered fresh ET (n = 73). Baseline characteristics, stimulation parameters, and cycle outcomes were compared between groups. A binary logistic regression analysis was established to identify independent predictors of clinical pregnancy. Results: The GnRHa-triggered group had significantly higher numbers of retrieved oocytes, mature (MII) oocytes, and fertilized oocytes compared to both hCG-triggered groups (p < 0.001). The number of obtained embryos and frozen embryos (good-quality embryos) was highest in the GnRHa group (p < 0.001). However, clinical pregnancy rates were comparable between the groups with a similar number and grade of transferred embryos (32.53%, 38.23%, and 32.87%, respectively). Multivariate regression analysis revealed that the grade of the transferred embryo was a significant predictor of clinical pregnancy (p = 0.034). Conclusions: This study provides insights into different triggering strategies for final oocyte maturation in PCOS patients. GnRH-agonist-triggered frozen-thawed cycles showed comparable clinical pregnancy outcomes to those of hCG-triggered cycles, with a potentially lower OHSS risk. The findings suggest that individualized triggering approaches based on patient characteristics and OHSS risk may be beneficial for PCOS patients undergoing IVF.