The invention provides a DNA (Deoxyribose Nucleic Acid) and protein level mutation analysis system, which comprises a reading and indexing judgment module and a mapping module, wherein the reading and indexing judgment module is used for readubg a gene mutation file, carrying out formatting processing on the gene mutation file to obtain a standard name, indexing a transcript sequence, gene information and gene transcript annotation information, constructing an amino acid codon corresponding correlation chart, and judging a mutation generation level and mutation mode, and judging whether mutation naming is protein level mutation or genome DNA level mutation or CDS (Coding Sequence) coding region mutation; and the mapping module is used for independently entering different level mutation mapping flows according to the judgment result of the reading and indexing judgment module to obtain the mapping relationship of three types of mutation naming. The system undertakes the phenotype relevant gene mutation and the polymorphic site of literature mining, and outputs the mapping relationship of various types of mutation naming so as to achieve a purpose of finishing the correspondence and the like of the gene mutation and the polymorphic sites of the pathopoiesia variation and the sequencing identification of the literature mining.