Background Birt-Hogg-Dube (BHD) syndrome is a rare autosomal dominant tumor syndrome caused by Folliculin (FLCN) gene mutation. The clinical manifestations are diverse, and the renal tumor is the most serious. Case presentation We report the case of a 51-year-old female with multiple space-occupying lesions in both kidneys, as well as bilateral renal cysts and multiple lung cysts. The resected tumors were finally diagnosed as bilateral renal hybrid oncocytic/chromophobe tumor (HOCT) and unilateral chromophobe cell carcinoma. A history of pneumothorax surgery 4 years ago was convinced. All of these strongly suggested the possibility of BHD syndrome. Gene test confirmed a heterozygous germline FLCN nonsense mutation (c.1429C > T, p.Arg477Ter). The patient is still doing well after 20 months of follow-up (cut-off date July 2022). Conclusion This is a case of BHD syndrome presented with bilateral renal tumor, renal cysts, and multiple lung cysts, and confirmed by gene testing. Patients with any combination of one or more of the manifestations should remain alert to the BHD syndrome. Our report will help to deepen the understanding of the clinicopathological features and molecular changes of BHD syndrome.