This study was aimed at investigating the prognostic ability of quantitative flow ratio (QFR) guided residual functional SYNTAX score (Q-rFSS) and functional incomplete revascularization (IR) in patients with ST-segment elevation myocardial infarction (STEMI) undergoing percutaneous coronary intervention (PCI).A total of consecutive 354 STEMI patients was included. Q-rFSS was defined as residual SYNTAX score (rSS) measured in vessels with QFR ≤0.8. At 2-year follow-up, functional IR (Q-rFSS≥1) showed significantly higher risk for major adverse cardiac events (MACE) than functional complete revascularization (CR) (Q-rFSS=0) (functional IR vs. CR, 22.0% vs. 7.4%; hazard ratio: 3.21; 95% confidence interval (Cl): 1.74 to 5.91; p<0.001). The area under curve (AUC) of Q-rFSS (0.738, 95% CI: 0.659 to 0.817) was significantly greater than that of rSS (0.648, 95% CI: 0.547 to 0.749). C-statistic for MACE increased from 0.656 (0.582 to 0.729) to 0.767 (0.705 to 0.829) after the addition of Q-rFSS to the clinical risk factors. Q-rFSS significantly improved risk classification compared with rSS (net reclassification improvement 0.439, 95% CI: 0.201 to 0.548; p<0.001).Functional IR is associated with higher risk of MACE during long-term follow-up in STEMI patients undergoing PCI. Q-rFSS has a better prognostic ability for the risk of MACE.