Liquid nitrogen freeze–thaw (LNFT) is an environmentally-friendly permeability enhancement technology. There are significant differences between shallow and deep coal in their composition and stress history. Therefore, it is necessary to reveal the difference in the impact of LNFT on the multistage gas flow between shallow and deep coal. In this paper, the differences in multistage gas flow were revealed from the perspective of a multiscale structure evolution, and the differences in the multiscale structure evolution were analyzed from the coal compositions and stress history. Nuclear magnetic resonance method was used in the multiscale structure evolution characterization. As for the multistage gas flow evolution, gas ad/de-sorption, diffusion, and seepage evolution characterization were investigated. There is a quadratic relationship between the total porosity and LNFT cycles in both shallow and deep coal. The fracture expansion is dominant in deep coal, while pores connectivity enhancement is dominant in shallow coal. The permeability of both shallow and deep coal increases during the LNFT cycling, presenting a logarithmic correlation between permeability and the number of cycles. With the same porosity, shallow coal has a higher permeability. LNFT cycling can improve the Langmuir volume. Langmuir volume and gas diffusion coefficients of deep coal is smaller both pre- and post-LNFT cycling. Except for CH4 in deep coal, the Langmuir pressure and gas diffusion coefficients in both coals are improved by LNFT cycling.