As the definitions of 36 atomic fragment types in organic compounds，multi-order atom-pair frequency matrix was constructed in terms of atomic fragments occurring in pair at different bond distances，and based on a new molecular coding technique as characteristic atom-pair hologram code（CAHC）proposed in this paper. Collected from reference reports，a large-scale ion mobility spectrometry collision cross section database comprising 819 samples was established and quantitative structure-spectrometry relationship（QSSR）studies were performed with the CAHC. Testing modeling stabilities and generalization abilities by both internal and external examinations confirmed that CAHC was in obvious linear relationship with peptide collision cross sections，while it was involved in partially nonlinear factors for a few polypeptides. The model was deemed to assist in quantitative computer-aided predictions for peptide collision cross sections.