The decrease of water transport capacity of lined canals in cold regions is mainly caused by frost heave failure of lining structure under freeze-thaw action. In view of this problem, the control measure of longitudinal joint setting in the canal plate was proposed and the numerical analysis was conducted. A thermal coupling frost heave model of concrete lined channel was constructed by treating the canal lining plate and frozen soil as a whole. Taking a concrete lined canal in Jingtai Irrigation District of Gansu Province as the research object, the influencing factors of frost resistance under three conditions were analyzed based on the contact constitutive of different joint construction measures and longitudinal joint filling. The results show that the depth of the bottom of the channel is not affected by the overall geometric boundary of the canal, but both the size of the canal boundary and the heat flow distribution of the subsoil have significant effects on the temperature field of the upper subsoil. The maximum freezing depth of the shady, bottom and sunny slopes of the canal are 86.3, 67.5 and 58.2 cm, respectively. Reasonable joint arrangement can reduce the normal frost heave force of the shady slope by up to 40.7%, the frost heave quantity of the bottom plate by up to 63.5%, and the tangential frost heave force by up to 43.8%, so that the frost heave distribution of the canal section tends to be uniform, and the model analysis is consistent with the measured results, indicating that the model established in this paper is reasonable. The results can provide a basis for the numerical calculation of long-distance water conveyance canals.