Aims To explore the effect of nonthrombotic internal jugular venous stenosis (IJVS) exerted on cerebral venous thrombosis (CVT). Methods Patients with imaging confirmed CVT were enrolled into this real-world case-control study consecutively from January 2018 through April 2021, and were divided into CVT and IJVS-CVT groups, according to whether or not with non-thrombotic IJVS. Chi-square and logistic regression models were utilized for between-group comparison of thrombotic factors. Results A total of 199 eligible patients entered into final analysis, including 92 cases of CVT and 107 cases of IJVS-CVT. Chi-square revealed that thrombophilic conditions were found in majority of CVT, while only minority in the IJVS-CVT group (83.7% vs. 20.6%, p < 0.001). Multivariate logistic regression indicated that most identified thrombophilia were negatively related to IJVS-CVT (all p < 0.05), including oral contraceptive use (beta = -1.38), hyperhomocysteinemia (beta = -1.58), hematology (beta = -2.05), protein C/S deficiency (beta = -2.28), connective tissue disease (beta = -1.18) and infection (beta = -2.77). All recruited patients underwent standard anticoagulation, 10 cases in IJVS-CVT group also received jugular angioplasty for IJVS correction. Most participants obtained alleviations during 1-year follow-up. However, both clinical and imaging outcomes in IJVS-CVT group were not as good as those in CVT group (both p < 0.05). Moreover, 8 cases with CVT and 7 cases with IJVS-CVT were rehospitalized for CVT recurrences and underwent customized treatment. Conclusion Nonthrombotic IJVS may be one of the risk factors of CVT. Anticoagulation might need to be suggested for IJVS patients.