The invention provides a method for analyzing a microbial population function by using metagenome data. The method comprises the following steps: collecting all known microbial species, gene and function information, and integrating the information as a reference database; sequencing the metagenome of the to-be-tested microbial specifies, controlling the sequencing data quality, computing speciesabundance and gene abundance, analyzing the composition difference of microbes among different samples and gene level difference; annotating the gene function, clustering the genes with the same function to obtain a function module, performing adduction computation on related abundance of all non-redundancy genes in various function modules to obtain abundance values of all function modules, performing difference comparison analysis or overall evaluation on the functions of the to-be-tested sample microbes. Through the method provided by the invention, the step of respectively comparing the splicing data, the assembling data, the predicting data and the sequencing data with the single function database is saved, the time is saved, the utilization efficiency of the sequencing data is improved, and the method can be used for analyzing high-throughput microbe whole-genome sequencing data and screening the function microbe.