We aim to explore the classifications based on coronary computed tomography angiography (CTA) for predicting the risk of major adverse cardiovascular events (MACE) in patients with suspected non-obstructive coronary artery disease (CAD) and compare with traditional non-obstructive CAD (NOCAD) classification, Duke prognostic NOCAD index, Non-obstructive coronary artery disease reporting and data system (NOCAD-RADS). 4378 consecutive non-obstructive CAD patients were assessed by coronary CTA for traditional NOCAD classification, Duke prognostic NOCAD index, NOCAD-RADS and a new classification (stenosis proximal involvement, SPI) from two medical centrals. We defined proximal involvement as any plaque was present in the main or proximal segments of coronary artery (left main, left anterior descending artery, left circumflex artery, or right coronary artery). The main outcome was MACE. During a median follow-up of 3.7 years, a total of 310 patients experienced MACE event. Kaplan–Meier survival curves showed the cumulative events increased significantly associated with traditional NOCAD, Duke NOCAD index, NOCAD-RADS and SPI classifications (allP< 0.001). In multivariate Cox regressions, the risk for the events increased fromHR1.20 (95% CI 0.78–1.83,P= 0.408) for SPI 1 to 1.35 (95% CI 1.05–1.73,P= 0.019) for SPI 2, using SPI 0 as the reference group. Coronary CTA based SPI classification provided important prognostic information for all cause-mortality risk and MACE prediction in patients with non-obstructive CAD, which was non-inferior than traditional NOCAD, Duke NOCAD Index and NOCAD-RADS classifications. The plaque location information by coronary CTA may provide additional risk prediction in patients with non-obstructive CAD.