Cryo-electron tomography (cryo-ET) is a powerful technique for visualizing the ultrastructure of cells in three dimensions (3D) at nanometer resolution. However, the manual segmentation of cellular components in cryo-ET data remains a significant bottleneck due to its complexity and time-consuming nature. In this work, we present a novel segmentation workflow that integrates advanced virtual reality (VR) software to enhance both the efficiency and accuracy of segmenting cryo-ET datasets. This workflow leverages an immersive VR tool with intuitive 3D interaction, enabling users to navigate and annotate complex cellular structures in a more natural and interactive environment. To evaluate the effectiveness of the workflow, we applied it to the segmentation of mitochondria in retinal pigment epithelium (RPE1) cells. Mitochondria, essential for cellular energy production and signaling, exhibit dynamic morphological changes, making them an ideal test sample. The VR software facilitated precise delineation of mitochondrial membranes and internal structures, enabling downstream analysis of the segmented membrane structures. We demonstrate that this VR-based segmentation workflow significantly improves the user experience while maintaining accurate segmentation of intricate cellular structures in cryo-ET data. This approach holds promise for broad applications in structural cell biology and science education, offering a transformative tool for researchers engaged in detailed cellular analysis.