Polyhydroxyurethane (PHU) is of major research interest because it is a non-isocyanate polyurethane-like (NIPU) polymer. Here, we demonstrate the ability to tune nanophase separation in linear, segmented PHU copolymers via the soft segment. PHUs were synthesized from polytetramethylene oxide (PTMO)- and polybutadiene-co-acrylonitrile (PBN)-based soft segments, with divinyl benzene dicyclocarbonate and Dytek-A as hard segment and chain extender, respectively. These NIPU polymers were characterized by small-angle X-ray scattering (SAXS), atomic force microscopy (AFM), dynamic mechanical analysis (DMA), differential scanning calorimetry (DSC), Fourier transform infrared spectroscopy (FTIR) and tensile testing. SAXS reveals that the NIPUs with 30–40 wt% hard segment are nanophase separated with interdomain spacings of 9–16 nm. DMA reveals that PTMO-based PHUs have broad interphases with a range of local compositions and glass transition temperatures (Tgs), with tan δ ≥ 0.3 over temperature ranges exceeding 70 °C in breadth. In contrast, PBN-based PHUs have sharper interphases, evidenced by narrow tan δ peaks near soft-segment and hard-segment Tgs as well as by DSC and AFM data. FTIR shows that the ratio of hydrogen-bonded carbonyl to free carbonyl is higher in PBN-based PHU than in PTMO-based PHU, consistent with the absence and presence of intersegment hydrogen bonding in PBN-based PHU and PTMO-based PHU, respectively.