Recent advances in cryo-electron microscopy (cryo-EM) instrumentation and single particle reconstruction have created opportunities for high-throughput and high-resolution three-dimensional (3-D) structure determination of virus. In order to visualize and effectively understand the 3-D structure, we present a display method based on surface rendering, which has the function of 3-D arbitrary region interactive segmentation and quantitative analysis, and integrate them into a software package called CEM-3DVDSS (cryo-EM 3-D virus display and arbitrary region segmentation system). CEM-3DVDSS consists of a complete set of modular programs for 3-D display and segmentation of icosahedral virus, which is organized under a graphical user interface and provides user-friendly options. First, we convert volume data in the MRC format obtained by cryo-EM single particle reconstruction to the format of our own software; in the preprocessing step, the original volume data are compressed and a better vector dimension is found for controlling the speed and detail of display. Then, the new volume data can be displayed and segmented using CEM-3DVDSS. We demonstrate the applicability of CEM-3DVDSS by displaying the 3-D structures of 2.5 nm (resolution) BmCPV (Bombyx mori cytoplasmic polyhedrosis virus), 2.5 nm CSBV (Chinese Sacbrood bee virus) and 1.4 nm C6/36DNV (Densonucleosis virus). As a result, both the 3-D display speed and signal-to-noise ratio of CEM-3DVDSS are improved compared with the original method, and the segmentation results become precise and more intact with additional function of quantitative analysis of 3-D structure.