Non-infectious cerebral venous thrombosis (CVT) is an uncommon type of cerebrovascular disease that usually affects young patients. It occurs frequently in female patients, probably due to the association of sex-specific risk factors for coagulopathies. Currently, the prognostic factors of CVT remain unclear. We retrospectively reviewed the clinical characteristics among 260 CVT patients, including 147 females and 113 males. A favorable clinical outcome was defined by the scores of the modified Rankin Scale (mRS) ≤ 2 at hospital discharge, while a poor clinical outcome was defined by an mRS score of 3 to 6. A headache (28.5%) was the most frequent presentation. The most commonly affected sinus was the transverse-sigmoid sinus (59.6%). Most of the cases (78.5%) were treated with anticoagulants. One hundred and fifty-seven patients (60.4%) were discharged with favorable clinical outcomes. Consciousness disturbance (odds ratio: 5.01, p < 0.001) was associated with a poor clinical outcome. Patients with poor clinical outcomes demonstrated higher D-dimer levels on admission (4137.76 ± 3317.07 vs. 2476.74 ± 2330.87 ng/mL FEU, p = 0.029) and longer hospitalization days (31.81 ± 26.29 vs. 13.96 ± 8.82 days, p < 0.001) compared with favorable clinical outcomes. These findings provide important information of clinical characteristics and prognosis for CVT. Aggressive monitoring and treatment should be considered in CVT patients with poor prognostic factors.