In order to explore the influence of cyclic freezing and thawing on the deformation characteristics of railway subgrade in seasonal frozen soil region, we performed freeze-thaw cycle test and consolidation compression test on the roadbed filling of Lanzhou-Xinjiang Railway as the research object. Through the tests we obtained the regularities of railway subgrade deformation caused by freeze-thaw cycles and compression characteristics. Moreover, we analyzed the influencing factors of compression characteristics by significance test via orthogonal analysis. Results revealed that the frost heave rate and the melting subsidence coefficient both increased in a power function with the increase of the number of freeze-thaw cycles, and both were positively correlated with water content and negatively correlated with compaction degree at the same freeze-thaw cycle. The compressive modulus of subgrade soil increased at first and then stabilized with the proceedings of cyclic freezing and thawing. The compaction degree (B) had the largest influence on compressive modulus, followed by water content (C), freeze-thaw cycle (A), the interaction between B and C, the interaction between A and B, and the interaction between A and C in sequence. We recommend choosing the compression modulus after nine freeze-thaw cycles as the design value of the road strength of Lanzhou-Xinjiang Railway. The research finding is of guiding significance for the prevention and control of frost heaving and subsidence of railway subgrade.