Non-invasive cardiac computed tomography angiography (CTA) is widely used to assess coronary artery stenosis and give clinical decision-making support to clinicians. The severity of stenosis lesion is commonly graded by a range of percent Diameter Stenosis (DS), which can introduce false positive diagnoses or over-estimation, triggering unnecessary further procedures. In this paper, a system and the associate methods to quantify stenosis by the percent Area Stenosis (AS) from cardiac CTA is presented. In the process, coronary artery tree is segmented and the centerline is extracted by Hessian filtering and the minimal path method. After a serial of 2D cross-sectional artery images along the artery centerline are obtained, lumen areas are segmented by ellipse-fitting with deformable models, and consequently to compute the lesion's AS. Experimental results on 5 CTA data sets show that compared to DS, AS better correlates to the reference standard for stenosis quantification, suggesting the efficacy of the proposed system.