Internal jugular vein stenosis (IJVS) has recently aroused increasing interests, whereas, the factors affecting its clinical outcomes are not clear. This study aims to explore the probable factors affected clinical prognosis by evaluating the IJVS with different etiologies and strategies. Patients with IJVS confirmed by contrast-enhanced magnetic resonance venography (CE-MRV) were enrolled from October 2017 through October 2018. One-year clinical outcomes of the IJVS cases enrolled in this study were assessed by outpatient and telephone follow-up using the Patient Global Impression of Change (PGIC) scores. According to the etiologies, patients were divided into thrombotic IJVS and non-thrombotic IJVS groups. And further, non-thrombotic IJVS group was divided into external compression and non-external compression subgroups. Outcomes of IJVS with different etiologies and strategies were compared and the probable prognostic factors were analyzed. A total of 118 eligible patients enrolled in this study, including 76 females and 42 males, mean aged 55.07±14.61 years. The average follow-up duration after discharge was 13.22±3.80 months. According to the PGIC scores, we categorized patients as good outcome and poor outcome groups. For thrombotic IJVS, patients underwent standard anticoagulant obtained remarkable PGIC improvement (100.0% vs. 33.3%, P=0.038). For non-thrombotic IJVS, stenting showed benefit in non-external compression subgroup (26.9% vs. 3.3%, P=0.019) but not in external compression subgroup. In addition, we found that in this Chinese IJVS cohort, poor outcomes involved old age (P=0.004), type 2 diabetes mellitus (P=0.036), previous hepatitis B virus (HBV) infection (P=0.027), and head noises (P=0.002). Multivariate logistic regression analysis indicated that continuous head noises [P=0.045, odds ratio (OR): 2.412, 95% confidence interval (CI): 1.019-5.711], as a unique symptom of IJVS may be significantly related to poor outcomes. In this Chinese cohort, elderly degenerative bone compression, type 2 diabetes mellitus, and previous HBV infection are the top-three probable etiologies of non-thrombotic IJVS and may involve poor outcome. Long-term head noises may predict IJVS and with poor outcome. Thrombosis-induced IJVS may get benefit from standard anticoagulation. Non-external compression IJVS can be corrected by stenting. 2019 Annals of Translational Medicine. All rights reserved.