Bone wax is a flexible hemostatic agent commonly used for surgery in the posterior cranial fossa to control bleeding from the mastoid emissary vein. A large amount of bone wax can migrate into the sigmoid sinus through the mastoid emissary canal (MEC). We aimed to identify clinical factors related to intraoperative bone wax migration through the MEC during microvascular decompression (MVD) surgery, which may result in sigmoid sinus thrombosis. We retrospectively collected the clinical data of patients with trigeminal neuralgia, hemifacial spasm, or trigeminal neuralgia accompanied by painful tic convulsif who underwent MVD. Basic information and the residual width and length (from the bone surface to the sigmoid sinus) of the MEC on computed tomography images were collected. We compared the collected clinical data between 2 groups of cases with and without intraoperative bone wax migration in the sigmoid sinus. Fifty-four cases with intraoperative bone wax migration and 187 patients without migration were enrolled. The t -test revealed significant differences in the width and length of the MEC ( P = .013 and P = .003, respectively). These variables were identified as significant factors in predicting intraoperative bone wax migration using multivariate logistic regression analysis. The large size of the MEC may be related to intraoperative bone wax migration into the sigmoid sinus in MVD. Neurosurgeons should be aware of these risks. Bone wax should be applied appropriately and hemostasis should be considered to control bleeding from the mastoid emissary vein in patients with a large MEC.