Abstract: In the process of reconstructing the three-dimensional structure of the virus by using the icosahedral symmetry of the virus, the existence of the symmetry-mismatch problem hindered the analysis of the real structure of the virus and the acquisition of the high-resolution structure. In order to eliminate the influence of symmetric mismatch on the three-dimensional structure of the virus, a symmetry-mismatch three-dimensional reconstruction algorithm by using the special subgroup search of the icosahedral point group was proposed. By taking the Grass Corp Reovirus (GCRV) as the experimental material, the three-dimensional structure of GCRV was obtained by using the three-dimension reconstruction technique of cryo-electron microscopy. Then, the orientation information was obtained through the local three-dimensional reconstruction and symmetry-mismatch searching, by adding the search of GCRV-specific vertex. The results showed that: the algorithm improved the efficiency of symmetry-mismatch orientation searching, and accurately reduced the orientation information of Grass Corp Reovirus (GCRV) by determining the icosahedral-specific apical position of the polymerase complex inside the virus. The results confirmed that the virus-deleted RdRp was in the pseudo-D3 symmetrical equatorial group, and it provided a new method for resolving the whole-virus symmetry-mismatch structure of double-stranded RNA virus and exploring the molecular mechanism of endogenous transcription of double-stranded RNA virus.