Venous malformation is a common congenital anomaly of vascular development, and endovascular sclerotherapy is currently the first-line treatment for it. Accurate puncture of the lesion is the key to endovascular treatment. Any deviation is likely to result in local ulcers, necrosis and other complications. We described one case, in which a newly developed real-time MRI navigation technology was introduced and sclerotherapy was successfully performed for deep lesions that were difficult to reach by conventional methods. This article reviewed the treatment process of this case, in order to provide guidance and help for venous malformations and other soft tissue diseases in the future.