Following studies of bulk behavior, the morphological evolution in thin films of linear TPUs with a high content of hard segment (HS) (from 70 to 100 wt %) on annealing is investigated. In contrast to melt-quenched bulk samples, a mixed phase was obtained for as-spin-cast films, and then, on annealing, a phase-separated mesophase domain, as previously observed by scattering and TEM in bulk samples, was observed by AFM to form directly from the mixed phase. In addition to this overall phase behavior, a crystallization behavior unique to thin films was observed: samples of thickness less than 120 nm and annealed at sufficiently high temperature developed large lamellar crystal blocks. Similar crystal blocks have also been found in thin films of a TPU with a more flexible chain extender, although in this case, with the greater HS/SS compatibility of this material, the phase separation behavior was not observed at all.