Abstract: The defects of saline soil subgrade are obvious along the southern Xinjiang Railway. The most serious cases occur at the railway section between Akesu and Kashi, 108 km in length. This kind of problem has been gradually found since the opening of the railway in 1999. The causes include local natural, engineering and hydrogeological conditions. The main defective forms are salinity exposure, surface expansion, subgrade compaction, sinking, track deformation, and so on. On the one hand, these defects increase the difficulty and workload of maintenance departments; on the other hand, they also seriously affect the traffic safety. An intelligent control test system is designed to study these problems. Its main functions are to investigate the secondary salinization phenomenon and transportation height of capillary water in the soil samples. The transport rules of water and salt are studied by means of the intelligent control test system based on two comparable cases of remolded saline and improved saline soils. The test results show that the secondary salinization phenomenon is not obvious in the improved saline soils. But the secondary salinization phenomenon is very obvious in the remolded saline soils under the same compression degree and physical condition. The secondary salinization degree gradually varies with the depth of soils. The Ⅲ-3 type improved saline soils on K938 are further tested parallelly. The results show that secondary salinization and the transportation height of capillary water can be controlled effectively if the fly ash, lime and cement are mixed into the saline soils with a certain proportion. The research results are successfully employed to solve the secondary salinization problem of the subgrade of southern Xinjiang Railway. There have been no new defects for more than 6 years.