The invention relates to a large-scale distributed parallel acceleration method and system for protein identification. The method comprises the following steps of: by a parallel processing method, theoretically digesting a protein sequence to obtain peptide sequences, and sorting and redundantly processing the peptide sequences so as to create a peptide index file block; sorting mass spectra spectrums, and evenly dividing the sorted mass spectra spectrums into a plurality of spectrum data blocks; and evenly distributing the spectrum data blocks to a plurality of host processes, and each host process sorting the distributed spectrum data blocks and sequentially assigning to idle slave processes for peptide spectrum matching identification; and summarizing identification results by the parallel processing method, inferring the corresponding protein sequences by the peptide sequences obtained by identification, and generating output files. When a processor has hundreds or even thousands of cores, the satisfactory acceleration efficiency when the protein identification is carried out can be obtained.