The invention discloses a method for data analysis of miRNA in animals with reference data based on a miRBase database. The method is characterized by comprising the following steps of preparation, filtration of logout data, genome alignment, small RNA annotation, miRNA feature analysis, miRNA expression quantity analysis, miRNA function and pathway analyses, and result sorting. The method disclosed by the invention has the beneficial effects that an analysis result is complete, and comprises involved miRNA analysis content and other detected small RNA information annotation, automated analysis is achieved, and statistics and sorting of all analysis content and results can be automatically and rapidly conducted only by providing related database information. All operation steps are visible, and thus errors can be conveniently checked, applied command lines and parameters and log results generated in operation can all be recorded when analysis is conducted step by step, and once a program fails during running, the errors can be rapidly queried.