To our knowledge, this is the first report of patient with BHD syndrome caused by a novel mutation in the FLCN gene who developed a cerebral venous sinus thrombosis(CVST).A 62-year-old male patient with a history of hypertension and two case of spontaneous pneumothorax. He had a 1-month history of headache and was admitted to the hospital one day after the headache aggravated. The patient had a family history of BHD syndrome which was confirmed by FLCN gene sequencing. Sequencing analysis revealed a novel nonsense mutation (NM_144997; c.607A > T; p.Lys203Ter) in the FLCN gene exon 6 of the patient, which was proved to be a pathogenetic mutation by pedigree verification. BHD syndrome was finally definitive diagnosis. Low molecular weight heparin (21 days) was given for anticoagulant therapy before and after resection of renal tumor which is confirmed to be clear cell carcinoma in the kidney. After discharge, warfarin was given for anticoagulant therapy (6 months).There was no recurrence of CVST. And no recurrence of tumor and new renal tumor were found in renal MRI examination after 6 months.