To explore the advantages and disadvantages of 3D Slicer reconstruction and 3D printing localization combined with transcranial neuroendoscope in the surgical treatment of deep cerebral micro cavernous hemangiomas. Method The clinical data of patients with deep cerebral micro cavernous hemangiomas treated by our hospital from June 2022 to February 2023 using 3D Slicer reconstruction and 3D printing localization technology combined with transcranial endoscopic surgery were retrospectively analyzed. A total of 5 cases with complete data were collected, including 2 males and 3 females, aged 9–59 years. All 5 patients had deep supratentorial cavernous hemangiomas with a diameter of less than 1.5 cm, and had clinical symptoms such as headache or epilepsy, and had been diagnosed by CT or MRI. Repeated bleeding from small cavernous hemangiomas in the deep brain can lead to clinical symptoms such as recurrent headache and epilepsy, and is required surgical treatment. However, cavernous hemangiomas often have smaller lesions and are difficult to locate in the deep part. Without neuronavigation, surgery can become extremely difficult. Our team’s newly developed 3D Slicer reconstruction and 3D printing localization technology which could provide new options for surgical treatment of small cavernous hemangiomas or other small lesions in the deep brain, but its accuracy and safety still need to be verified by further clinical research.