Polysiloxanes have attracted considerable attention in biomedical engineering, owing to their inherent properties, including good flexibility and biocompatibility. However, their low mechanical strength limits their application scope. In this study, we synthesized a polysiloxane-based polyurethane by chemical copolymerization. A series of thermoplastic polysiloxane-polyurethanes (Si-TPUs) was synthesized using hydroxyl-terminated polydimethylsiloxane containing two carbamate groups at the tail of the polymer chains 4,4′-dicyclohexylmethane diisocyanate (HMDI) and 1,4-butanediol as raw materials. The effects of the hard-segment content and soft-segment number average molecular weight on the properties of the resulting TPUs were investigated. The prepared HMDI-based Si-TPUs exhibited good microphase separation, excellent mechanical properties, and acceptable repeatable processability. The tensile strength of SiTPU-2K-39 reached 21.5 MPa, which is significantly higher than that of other flexible polysiloxane materials. Moreover, the tensile strength and breaking elongation of SiTPU-2K-39 were maintained at 80.9% and 94.6%, respectively, after three cycles of regeneration. The Si-TPUs prepared in this work may potentially be used in gas separation, medical materials, antifouling coatings, and other applications.