Background The computational fluid dynamics(CFD) approach has been frequently applied to compute the fractional flow reserve(FFR) using computed tomography angiography(CTA). This technique is efficient. We developed the DEEPVESSEL-FFR platform using the emerging deep learning technique to calculate the FFR value out of CTA images in five minutes. This study is to evaluate the DEEPVESSEL-FFR platform using the emerging deep learning technique to calculate the FFR value from CTA images as an efficient method. Methods A single-center, prospective study was conducted and 63 patients were enrolled for the evaluation of the diagnostic performance of DEEPVESSEL-FFR. Automatic quantification method for the three-dimensional coronary arterial geometry and the deep learning based prediction of FFR were developed to assess the ischemic risk of the stenotic coronary arteries. Diagnostic performance of the DEEPVESSEL-FFR was assessed by using wire-based FFR as reference standard. The primary evaluation factor was defined by using the area under receiver-operation characteristics curve(AUC) analysis. Results For per-patient level, taking the cut-off value ≤ 0.8 referring to the FFR measurement, DEEPVESSEL-FFR presented higher diagnostic performance in determining ischemia-related lesions with area under the curve of 0.928 compare to CTA stenotic severity 0.664. DEEPVESSEL-FFR correlated with FFR(R = 0.686, P < 0.001), with a mean difference of-0.006 ± 0.0091(P = 0.619). The secondary evaluation factors, indicating per vessel accuracy, sensitivity, specificity, positive predictive value, and negative predictive value were 87.3%, 97.14%, 75%, 82.93%, and 95.45%, respectively. Conclusion DEEPVESSEL-FFR is a novel method that allows efficient assessment of the functional significance of coronary stenosis.