The vertebral artery’s morphological characteristics are crucial in spontaneous vertebral artery dissection (sVAD). We aimed to investigate morphologic features related to ischemic stroke (IS) and develop a novel prediction model. Out of 126 patients, 93 were finally analyzed. We constructed 3D models and morphological analyses. Patients were randomly classified into training and validation cohorts (3:1 ratio). Variables selected by LASSO — including five morphological features and five clinical characteristics — were used to develop prediction model in the training cohort. The model exhibited a high area under the curve (AUC) of 0.944 (95%CI, 0.862–0.984), with internal validation confirming its consistency (AUC = 0.818, 95%CI, 0.597–0.948). Decision curve analysis (DCA) indicated clinical usefulness. Morphological features significantly contribute to risk stratification in sVAD patients. Our novel developed model, combining interdisciplinary parameters, is clinically useful for predicting IS risk. Further validation and in-depth research into the hemodynamics related to sVAD are necessary.