This study aims to create a learning environment equivalent to real animal dissection by employing a 3D virtual reality (VR) simulation in a metaverse-based anatomical experiment. With the increasing flexibility of hand-tracking manipulation in VR, it is essential to understand how manipulating 3D objects in science simulations impacts students' cognitive load, virtual presence, and spatial ability. Therefore, this research examines hand-tracking's effects on college students' virtual presence, cognitive load, and spatial ability. A pre-posttest control group design will be applied to approximately 40 right-handed college students. All participants will engage in HMD-wearing learning within a metaverse platform for validation purposes. Each dependent variable will be measured using surveys and brainwaves, with one-way multivariate analysis of variance (MANOVA) in SPSS and machine learning techniques. This research could contribute to the development of more effective educational experiences by identifying the factors that positively or negatively influence virtual presence, cognitive load, and spatial ability.