X-ray transparency occurs during the interaction of X-ray free electron laser with matter. The study of the mechanism of X-ray transparency is of great value for understanding the interaction between X-ray free electron laser and matter. In this paper, the main ionization modes from neutral neon atom till bare nucleus at different flux densities are determined based on the 2000 eV photoionization cross sections and the Auger decay rates of various neon atoms (ions), calculated by the Flexible Atomic Code program. By establishing and solving the rate equations, the formulas of the proportions of various electronic configurations of neon in the main ionization mode are obtained. The proportions of electron configurations in the main ionization modes and the atomic average photoionization cross sections at flux densities of 2000 and 10000 -2fs-1 are calculated by using the formulas. The ratios of the number of hollow atoms to that of complete valence electrons at any time under different flux density laser irradiations are calculated. It is found that both the bare nuclei and the hollow atoms cause X-ray transparency, and a relatively high ratio of the number of hollow atoms to that of complete valence electrons can be achieved by choosing appropriate flux density and pulse duration.