Ballastless track of high-speed rail has a very strict requirement for expansion deformation value, for the expansion-shrinkage deformation caused by flooding of foundation expansion mudstone will threaten the driving security and comfort. To study the attenuation law of expansion rate and moisture migration rate of mudstone with the increase of horizontal distance and depth of flooding position, a typical expensive mudstone of the second double track of Lanzhou-Xinjiang Railway is taken as the object of study, and three groups of remolding mudstone deformation testing on the top and side are conducted with two methods of flooding. The test results show that as the horizontal length to flooding pipe is different, the expansion-travel curve has different change rules: the further the horizontal length to flooding pipe is, the slower the expansion rate is, and the smaller the moisture migration rate is; during the lateral flooding, the expansion of bottom soil mass will be caused firstly along the direction of depth. Through further analysis on the test data, it is proposed to analyze the attenuation law of moisture migration rate with initial average permeability coefficient, and it is known through calculation that the moisture migration rate shows a tendency of attenuation with the increase of distance to flooding pipe and also with the increase of depth. The research results can provide a theoretical support for control and early warning of foundation mudstone arching-up.