The use of diameter stenosis (DS), as revealed by coronary angiography, for predicting fractional flow reserve (FFR) usually results in a high error rate of detection. In this study, we investigated a method for predicting FFR in patients with coronary stenosis based on multiple independent risk factors. The aim of the study was to improve the accuracy of detection. First, we searched the existing literature to identify multiple independent risk factors and then calculated the corresponding odds ratios. The improved analytic hierarchy process (IAHP) was then used to determine the weighted value of each independent risk factor, based on the corresponding odds ratio. Next, we developed a novel method, based on the top seven independent risk factors with the highest weighted values, to predict FFR. This model was then used to predict the FFR of 253 patients with coronary stenosis, and the results were then compared with previous methods (DS alone and a simplified scoring system). In addition to DS, we identified a range of other independent risk factors, with the highest weighted values, for predicting FFR, including gender, body mass index, location of stenosis, type of coronary artery distribution, left ventricular ejection fraction, and left myocardial mass. The area under the receiver-operating characteristic curve (AUC) for the newly developed method was 84.3% (95% CI: 79.2–89.4%), which was larger than 65.3% (95% CI: 61.5–69.1%) of DS alone and 74.8% (95% CI: 68.4–81.2%) of the existing simplified scoring system. The newly developed method, based on multiple independent risk factors, effectively improves the prediction accuracy for FFR.