Objective: To elucidate whether DNA aneuploidy was an independent discriminator for carcinoma within oral potentially malignant disorders (OPMDs), and further establish and validate a risk model based on DNA aneuploidy for the detection of oral cancer. Methods: A total of 810 consecutive patients with OPMD were prospectively enrolled from March 2013 to December 2018, and divided into a training set (n = 608) and a test set (n = 202). Brushing and biopsy samples from each patient were processed by DNA-DNA image cytometry and histopathological examination, respectively. Results: DNA aneuploidy of an outside DNA index ≥ 3.5 in OPMD was an independent marker strongly associated with malignant risk [adjusted odds ratio: 13.04; 95% confidence interval (CI): 5.46–31.14]. In the training and test sets, the area under the curve (AUC) was 0.87 (95% CI: 0.82–0.91) and 0.77 (95% CI: 0.57–0.97), respectively, for detecting carcinoma in OPMD patients. The independent risk factors of lateral/ventral tongue and non-homogenous type combined with a risk model built with a multivariate logistic regression revealed a more favorable diagnostic efficacy associated with the training set (AUC: 0.93; 95% CI: 0.91–0.96) and test set (AUC: 0.94; 95% CI: 0.90–0.98). The sensitivity and specificity of carcinoma detection within OPMD was improved to 100% and 88.1%, respectively. Conclusions: This large-scale diagnostic study established a risk model based on DNA aneuploidy that consisted of a noninvasive strategy with lateral/ventral tongue and non-homogenous features. The results showed favorable diagnostic efficacy for detecting carcinoma within OPMD, irrespective of the clinical and pathological diagnoses of OPMD. Multicenter validation and longitudinal studies are warranted to evaluate community practices and clinical applications.