[Objective]This paper aims to make a bioinformatics analysis on the subcellular localization and functional site of CagM protein in helicobacter pylori cag pathogenicity island and further explore the functions of CagM protein. [Methods]Apply SubLoc v1.0 program to make the subcellular localization of this protein, and use TargetP program and PSORTb version 2.0.4 to make the verification and analysis; use ANTHEPROT 5.0, Gene3D Scan Sequence software and InterPro Scan software to analyze the functional site of CagM protein, and use DOG1.0 software for the drawing. [Results]CagM is a kind of secretory protein located in the periplasmic space rather than a membrane protein; CagM has many functional sites such as N-glycosylation site, protein kinase C phosphorylation site, tyrosine kinase phosphorylation site, and myristoylation acting site as well as many PDZ III binding sites. [Conclusion]As a kind of secretory protein located in the periplasmic space, CagM protein will become the substrate of many kinds of kinases after the translation and a series of modification, and after it is activated, it will participate in the signal transmission function and the assembly of IV type secretion system, which may play a role in the collection and assembly process of other proteins.