Mudstone is a very common rock that, when in contact with water, can exhibit considerable volume change and breakdown. This behavior of mudstone is frequently encountered in geotechnical engineering and has a considerable influence on infrastructure stability. This is particularly important in the present work, which focuses on mitigating the harmful properties of mudstone. The samples studied are of Permian Age mudstone from Shandong Province, China. Modification tests using organic silicone additive material were carried out. The mechanisms of physical properties modification of mudstone were comparatively studied using corresponding test methods, and the modification mechanism of organic silicone additive material acting on mudstone was analyzed. The following conclusions were drawn. The surface texture and characters of mudstone changed dramatically, surface character turns from hydrophilic to hydrophobic after organic silicone additive material modification. The changes in the surface character indicate a reduction in the water sensitivity of mudstone. After modification, the shape of porosity and fracture of mudstone changed unremarkable, and the total and free expansion ratios decreased obviously, whereas the strength increased markedly.