Thermoplastic polyurethanes (TPUs) have received considerable attention because of their flexible structure and comprehensive performance. 3,3-Dimethyl-4,4'-diphenyl diisocyanate (TODI) was first introduced to fabricate high-performance TPU by tailoring the mole ratio of the hard segment to the soft segment and the molecular weight of the soft segment for three-dimensional (3D) printing. The influence of the microstructure on glass transition temperature, tensile strength, modulus, loss factor, and softening temperature was investigated. The annealing process was proved to increase the degree of microphase separation of TODI-based TPU. Compared with TPU derived from widely commercialized isocyanates, our prepared TODI-based TPU exhibited remarkably high heat resistance. In addition, it is worth noting that our TODI-based TPU prepolymer has long-term and stable storage, which is beneficial for industrial application. This work is crucial to fabricate new TPU elastomer materials with high heat resistance for 3D printing and evaluate the structure-property behavior of TODI-based TPU, which could help other researchers design TODI-based TPU.