The invention discloses a rapid analysis method based on an OrthoMCL clustering result, and belongs to the field of comparative genomics and bioinformatics. The method is based on an OrthoMCL clustering result and comprises the steps of: establishing automatic identification of various proteins in generic analysis, including all representative proteins, core proteins, single-copy core proteins andspecies-specific proteins; based on the respective classification of the proteins, counting the number of the classified proteins existing in the respective species, and outputting the result according to the category. The method achieves output of representative sequences of proteins in various classifications and output of representative sequences of various proteins in each species. In addition, according to the method, protein homologous clustering results are output according to the sequence corresponding to each homologous protein, and a foundation is laid for achieving higher-level personalized analysis in generic analysis.