Objective: This study aimed to evaluate the effectiveness of flexible bronchoscopy (FB)-assisted extubation compared to conventional extubation strategies in managing extubation failure (EF) in infants after congenital heart disease (CHD) surgery. Methods: A historical control study included 95 infants who underwent CHD surgery between May 2021 and May 2023. Patients were divided into two groups based on the postoperative extubation management strategy: the conventional weaning (CW) group (n=45) received management without FB assistance to prevent EF, and the FB group (n = 50), where FB was actively utilized to facilitate extubation. Results: The FB group demonstrated a significantly lower reintubation rate than the CW group (4% vs. 18%, p = 0.043). Additionally, the FB group exhibited shorter durations of mechanical ventilation, noninvasive ventilation (NIV), and hospital stays (p < 0.05). No significant differences between groups in EF rates (14% vs. 18%, p = 0.779) or extubation-related complications were observed. Findings relating to FB-assisted extubation identified subglottic stenosis, airway granulation, and mucus plug obstruction as common contributors to EF, facilitating targeted interventions. Conclusions: FB-assisted extubation may reduce reintubation rates and hospital stays in infants after CHD surgery without increasing complication risks; however, further studies are needed to validate these findings.