MALDI MS has been widely used in the analysis of biomolecules including nucleic acids, peptides, proteins and oligosaccharides. However, after more than 20 years of research, the mechanism of gas phase ion formation in the process of MALDI is still under debate. In most of models proposed in the literature, free ions in the plume were assumed before the application of the ion extraction potential, which implies or gives the impression of an overall charge unbalanced plume. In this article, the ion pair thermal model is presented. Key assumptions of the model include thermal desorption and ionization, strong tendency to gas phase neutralization, ion pair formation, overall charge balanced plume and thermal equilibrium. Based on the assumptions, attempts are made to provide detailed estimations on the quantities of ions in the gas phase available for extraction and detection by the mass spectrometer. The estimations are conducted both at the macroscale and individual ion pair levels. The ion yields derived from the analyses are close to but somewhat lower than experimental data. This may suggest that the preformed ions in the solid sample, the quantities of which are also estimated, ejected into the plume may not completely reach thermal equilibrium in the gas phase and may contribute a portion of the ions that are extracted and detected by the mass spectrometer.