To mitigate the cracking of concrete lining in cold regions, the impact of replacing in-situ clay with cement-stabilized soil on the frost-heave deformation of channel foundations was investigated. The temperature and deformation patterns during the freeze-thaw process of Ningxia clay and cement-stabilized soil were examined in a self-made soil specimen freeze-thaw apparatus and a channel freeze-thaw model device. It is found that the freeze-thaw deformation of the clay specimens is driven by expansion upon freezing and settlement upon thawing, with the cumulative expansion demonstrating a linearly increasing trend with the number of freeze-thaw cycles. In contrast, the freeze-thaw deformation of the cement-stabilized soil specimens exhibits a pattern of contraction upon freezing and expansion upon thawing, with low deformation magnitudes and negligible cumulative deformation observed after multiple cycles. An 1∶1 scale model experiment of the channel revealed that the use of cement-stabilized soil in channel construction could reduce the amplitude of freeze-thaw deformation by more than half compared to the use of clay, thereby enhancing the resistance to frost-heave deformation. It can be concluded that partially replacing clay with cement-stabilized soil could reduce the amplitude of channel freeze-thaw deformation and thereby relieve the risk of cracking in channel concrete lining.