Using three-dimensional (3D) contents for learning virtual reality (VR) is the use of 3D graphic systems in combination with various devices to provide the effect of immersion in the interactive virtual environment. In this study, the authors built a Virtual Body Structures Auxiliary Teaching System (VBS-ATS) based on situated learning and virtual reality theory. This system is a Web-based three-dimensional interactive learning environment that can be used for assisting students to learn human structure. In addition, this system consists of six learning units including Nervous System, Respiratory System, Vascular System, Digestive System, Urinary System, and Skeletal System of a human body. The main purpose of this study attempts to evaluate learners’ perceptions on 3D virtual reality applied in medical education. The instructor uses project virtual reality to present 3D course contents in the classroom. To improve interactivity, learners can use the Web-based 3D learning system through desktop virtual reality to assist their learning when they need. Three research variables: perceived usefulness, perceived easy to use and intention to use, are investigated in this study. Finally, a questionnaire, based on Technology Acceptance Model (TAM), was developed for evaluating this 3D VR learning environment. Results indicated that perceived easy to use can predict perceived usefulness. Moreover, perceived easy to use and perceived usefulness can predict students’ intention to use the 3D virtual reality system. In addition, perceived usefulness accounts for 49% of variance in intention to use the system.