The invention provides a method for analyzing data of prokaryotic proteogenomics rapidly and automatically. Users only need to provide mass spectral data and a corresponding database file and set a simple retrieval parameter; retrieval of data of proteogenomics can be completed; simultaneously, a user defined data retrieval result can also be compatible; therefore, the identification coverage rate of the data of proteogenomics is increased; in the method disclosed by the invention, library search engines of different algorithms are integrated in advance; disadvantages of a single retrieval method are made up; a user defined library search result can also be compatible; the method has good compatibility; the peptide fragment identification coverage rate is increased to the most extent; in the method disclosed by the invention, functional annotation of new genes is automatically completed; large-scale identification of protein post-translational modification and analysis of non-labelled quantitative proteomics are realized for the first time; and automatic and rapid deep analysis of the data of proteogenomics is really realized.