This paper aimed to explore segmentation effects of the magnetic resonance imaging (MRI) images of the inner auditory canal of patients with Meniere’s disease under the intelligent segmentation method of the inner ear based on three-dimensional (3D) level set (IS3DLS). The statistical shape model and the level set segmentation algorithm were combined to propose the IS3DLS. First, the shape training samples of the inner ear model were determined, and the results were manually segmented to further obtain region of interest (ROI) of the inner ear. The IS3DLS was employed to accurately segment MRI images of the inner auditory canal of patients with Meniere’s disease. The segmentation performance of IS3DLS was compared with the expert manual segmentation method and the region growth level set-based segmentation algorithm. Results showed that Matthews correlation coefficient (MCC), Dice similarity coefficient (DSC), false positive rate (FPR), and false negative rate (FNR) of this algorithm were 0.9599, 0.9594, 0.0325, and 0.03655, respectively. Therefore, the IS3DLS could achieve good segmentation effect in MRI images of the inner auditory canal of patients with Meniere’s disease, which was helpful for diagnosis and subsequent treatment of Meniere’s disease.