The emission behavior of polyatomic ions Cs2Cl+ and Cs2BO2+ in the presence of various carbon materials (Graphite, Carbon, SWNTs, and Fullerenes) in the ionization source of thermal ionization mass spectrometry (TIMS) has been investigated. The emission capacity of various carbon materials are remarkably different as evidenced by the obvious discrepancy in signal intensity of polyatomic ions and accuracy/precision of boron and chlorine isotopic composition determined using Cs2Cl+-graphite-PTIMS/Cs2BO2+-graphite-PTIMS methods. Combined with morphology and microstructure properties of four selected carbon materials, it could be concluded that the emission behavior of the polyatomic ions strongly depends on the microstructure of the carbon materials used. A surface-induced collision mechanism for formation of such kinds of polyatomic ions in the ionization source of TIMS has been proposed based on the optimized configuration of Cs2BO2+ and Cs2Cl+ ions in the gas phase using a molecular dynamics method. The combination of the geometry of the selected carbon materials with the configuration of two polyatomic ions explains the structure effect of carbon materials on the emission behavior of polyatomic ions, where graphite samples with perfect parallels and equidistant layers ensure the capacity of emission to the maximum extent, and fullerenes worsen the emission of polyatomic ions by bloddng their pathway.