Seepage in loess is generally a two-phase water and gas flow transport process, during which the migration of compressed high pore pressure (greater than atmospheric pressure) bubbles has a non-negligible effect on the loess structure. Therefore, in this study, the unsaturated seepage test of small loess soil columns under different working conditions was conducted, and the scanning electron microscope test was carried out on the loess under each test condition. By comparing and analyzing the experimental results, the effect of high pore pressure bubble migration on the seepage and structure of the soil during the seepage process was investigated. It was found that in the infiltration process, the seepage time increased sharply with the increase of density, and because of the hindering effect of gas in the infiltration process, there was a time difference in the seepage process of the specimens under the same dry density and different test conditions, and the larger the dry density the smaller the percentage of this time difference. We also found that at the same dry density, with the increase of high pore pressure bubble content, the pore content of the soil increases, and the greater the dry density, the greater the effect caused by gas transportation.