The objective of this study is to evaluate the effectiveness of interactive Mixed Reality (MR) learning and compare it to traditional methods for independently learning inner ear anatomy through two experiments. The evaluation was conducted using HoloInnerEar, our new interactive MR tool for inner ear anatomy learning. In the first controlled experiment (N = 32), we compared independent learning techniques for normal anatomy using the interactive 3D + 2D features of HoloInnerEar to the traditional method using a video course combined with a mobile medical imaging application. Results show that interactive MR learning is significantly better than the traditional method for the interest of learning and knowledge confidence, and yields better knowledge test scores on multiple tasks, although not reaching statistical significance. In a second experiment, the malformation learning module of multiple-linked views of HoloInnerEar was assessed with otolaryngologists (N = 7). Experts agreed that this module fills a gap in inner ear malformation learning, which is important yet overlooked in the current curriculum. Positive feedback is obtained through a customized questionnaire and the NASA Task Load Index (NASA-TLX). Overall, we believe that interactive MR learning is a promising complementary approach to learning the anatomy of normal and malformed inner ears alike.