The purpose of the study was to evaluate the optimal cut-off value of CT-Fractional Flow Reserve (CT-FFR) using fluid–structure interaction and how to adjust the CT-FFR’s underestimation from a standpoint of minimize 1-year cardiac events. Subjects were 38 cases with 44 vessels in which stenosis of 30–90% was detected using one-rotation scanning by 320-row coronary CT angiography (CCTA) and invasive FFR (i-FFR) was performed within subsequent 90 days. CT-FFR was calculated using on-site from the multiple cardiac phases. A hypothetical 1-year cardiac event incidence was estimated using previous evidences when revascularization was decided based on CT-FFR. We assessed the optimal cut-off value of CT-FFR and how to correct the CT-FFR to minimize hypothetical cardiac events under four different disease prevalence (20%, 25%, 30%, 35%, and 40%). A total of 16 vessels had i-FFR ≤ 0.8. On per-patient basis, the sensitivity, specificity, positive predict value, negative predict value, and diagnostic accuracy of CT-FFR ≦ 0.8 vs CCTA > 50% to detect functional stenosis defined as invasive FFR ≦ 0.80 were 93.3% vs 73.3%, 73.9% vs 26.1%, 70.0% vs 39.3%, 94.4% vs 60.0%, and 81.6% vs 44.7%, respectively. For minimize 1-year cardiac events, the optimal cut-off value for more than 30% of disease prevalence was 0.80. However, the optimal cut-off value for 20, 25, and 30% was 0.54 in any cases. After the adjustment of CT-FFR using a formula of 0.3X + 0.634 for CT-FFR < 0.7 to counteract its underestimation, the % reduction of the events for 20, 25, 30, 35, and 40% at a 0.80 cut-off were 19.0%, 15.6%, 12.6%, 10.0%, and 7.7% respectively. It was reasonable to support that the optimal cut-off value was 0.80 in disease prevalence of more than 30% for minimize 1-year cardiac events. However, underestimation should be adjusted to reduce cardiac events, especially when disease prevalence is low.