Background: Obstructive sleep apnea hypopnea syndrome (OSAHS) constitutes an independent factor for high warfarin dose for patients with pulmonary embolism (PE). The aim of this study was to investigate whether the 6-month anticoagulation treatment by warfarin is enough for patients with PE complicated by OSAHS. Methods: We investigated 97 PE patients, 32 of them had OSAHS and 65 non-OSAHS. Warfarin was administered for 6-month if no abnormal circumstances occurred. All patients were followed up for 18 months. Adverse events (AE) included death, major bleeding, hospitalization due to heart failure or pulmonary hypertension, and recurrence or aggravation of PE (including deep vein thrombosis). Recurrence rate of PE after warfarin cessation was compared between the two groups. Results: OSAHS patients required a significantly higher dose of warfarin than their non-OSAHS counterparts (4.73 mg vs. 3.61 mg, P < 0.001). During warfarin treatment, no major bleeding and aggravation of PE occurred among OSAHS patients, and the rates of various AE were not significantly different between the OSAHS and non-OSAHS groups. PE recurrence was higher in OSAHS than non-OSAHS groups after withdrawal of warfarin (21.43% vs. 6.78%, P = 0.047). Compared with non-OSAHS patients, OSAHS group had lower international normalized ratio (INR) value but higher plasminogen on baseline and INR resumed to a relatively low level after warfarin discontinuation. Conclusions: OSAHS patients may present with hypercoagulation and relatively high-risk of recurrence of PE after cessation of 6-month warfarin treatment.