The invention provides a crosslinking dipeptide rapid identification method, comprising: 1) extracting effective spectrum peaks in a to-be-identified series-connected spectrogram, according to mass corresponding to each effective spectrum peak, searching a fragment index, to obtain a corresponding peptide fragment sequence as a candidate [alpha] peptide sequence, wherein the fragment index records mass of each fragment and the peptide fragment sequence corresponding to the mass of each fragment; 2) for each candidate [alpha] peptide sequence, according to parent ion mass of the to-be-identified series-connected spectrogram, calculating corresponding [beta] peptide mass, to obtain a corresponding candidate [beta] peptide sequence, combining the candidate [alpha] peptide sequence with the corresponding candidate [beta] peptide sequence, to obtain candidate crosslinking dipeptide; 3) matching the candidate crosslinking dipeptide obtained in the step 2) with the series-connected spectrogram in a fine manner, to obtain an identification result. The method does not need to use a special cross-linking agent, searching speed is fast, identification efficiency is high, and search sensitivity is high.