The emission behavior of polyatomic ions in the ionization source of thermal ionization mass spectrometry (TIMS) was investigated. The results Suggest that the presence of a graphite promoter plays a key role for the formation and stable emission of polyatomic ions, such as M2X+, M2BO2+, Cs2NO2+, and Cs2CNO+. Our data further implied that the intensity of M2X+ and M2BO2+ increases and the emission temperature decreases with increasing cationic and anionic radius. During the boron isotopic measurement using the Cs2BO2+-graphite-PTIMS method, the isobaric interference ion Cs2CNO+ cannot be transformed from nitrate or organic compounds containing an amide group but can be induced by the existence of trace amounts of boron because of its special electron-deficiency property (B3+). Characterization on the planar crystalline structure of various graphite samples with SEM, TEM, and Raman spectroscopy confirmed the relationship of the emission capacity of polyatomic ions and the crystal microstructure of graphite and provides direct evidence that graphite with a perfect parallel and equidistant layer orientation shows a beneficial effect on the emission of polyatomic ions in TIMS. The mechanism study on the formation of polyatomic ions opens the possibility to establish high precision methods for isotopic composition analysis of more nonmetal elements with the TIMS technique.