BACKGROUND: Quantitative flow ratio (QFR) and target-vessel SYNTAX score (tvSS) are novel indices used to assess lesion physiology and morphology in percutaneous coronary intervention (PCI). Their prognostic implication after successful recanalization of coronary chronic total occlusion (CTO) is unknown. OBJECTIVES: To investigate the prognostic value of QFR measured immediately after successful CTO-recanalization in predicting vessel-oriented adverse events, and to compare it with the pre-procedural morphological tvSS. METHODS: QFR was measured offline after successful CTO-PCIs in a single center. We grouped the patients according to a cut-off value of post-PCI QFR (0.91). The primary outcome was target-vessel failure (TVF) at 2 years. RESULTS: Among 470 CTO lesions performed during the study period, 324 were eligible for QFR analysis (258 with QFR ≥ 0.91 and 66 with QFR < 0.91). The mean age of the study population was 68.3 ± 10.7 years. The low QFR group had a lower left ventricular ejection fraction (45.8 ± 13.9% vs. 49.8 ± 12.4%, p = 0.025) and a higher rate of atrial fibrillation (19.7% vs. 11.2%, p = 0.020). The mean tvSS was 12.8 ± 4.8, and it showed no significant difference in both groups (13.6 ± 5.1 vs. 12.6 ± 4.6, p = 0.122). Patients with low post-CTO QFR had a trend to develop more TVF at 2 years (21.2% vs. 12.4%, HR 1.74; 95% CI 0.93-3.25, p = 0.086). Low post-CTO QFR failed to predict 2-year TVF (aHR 1.67; 95% CI 0.85-3.29, p = 0.136), while pre-procedural tvSS was an independent predictor for 2-year TVF (aHR 1.06; 95% CI 1.01-1.13, p = 0.030). CONCLUSION: We found a limited prognostic value of immediate physiological assessment using QFR after successful CTO intervention. Pre-procedure morphological characteristics of CTO lesions using tvSS can play a role in predicting long-term adverse events.